++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Saving rotated PDB files
Date: Thu, 01 Jan 1998 12:10:30 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

On Dec 26 I announced a comparison of the PDB editing capabilities and
limitations of RasMol, Chime and Weblab at

http://www.umass.edu/microbio/rasmol/pdbtools.htm

Nicolas Guex has now kindly provided information for his Swiss-PDBViewer.
The good news is that it can save ROTATED AND TRANSLATED COORDINATES WITH
ORIGIN OF USER CENTER, and that is controlled by disabling a menu option
'Save in original orientation'. You can save selected residues (evidently
not atom by atom selections?) as well.  Further details have been added to
the above web page. Among the packages compared, this is currently the only
freeware with such capabilities.

Earlier parts of this thread on our list are on Dec 14 and Dec 15 as well
as Dec 26.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Nav4.04 SOLUTION! Absolute javascript references needed.
Date: Thu, 01 Jan 1998 13:17:19 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

On Dec 30 I reported here that some of my Chime web sites which work under
Win95 with Chime 1.0/2.0beta1 Navigator 4.01 fail under Navigator 4.04.

Bryan van Vliet of MDL was kind enough to track down the problem and come
up with a solution.  It appears that Nav4.04 is less forgiving about
javascript references in a multi-frame page.  Whether this might be relaxed
in Nav4.05 (not yet available) is unclear.

Although the embed tag which invokes Chime in my code is in the same frame
as the javascript include which defines the messagecallback function,
Nav4.04 requires that the frame where the function is defined be explicit
('absolute').  So, my invocation

<embed src="1atom.pdb" bgcolor="#000000"
  align=left
  height=100% width=30%
  hspace=10
  debugscript=on
  name="chime_graphics"
  MessageCallback="ChimeMsg">

fails to allow messages to reach ChimeMsg(), javascript reporting that
ChimeMsg() is undefined.  Changing the last line above to

  MessageCallback="top.fr_chime.ChimeMsg">

works! (Thanks to Bryan!)  'top' is a generic reference to the top level of
the current window.  'fr_chime' is the name I assigned (in the frameset) to
the frame which contains in its header

<script src="chim3way.js"></script>

where the function ChimeMsg() is defined. Despite the fact that it is the
same frame containing the <embed ...>, Nav4.04 requires an absolute reference.

This explains why my 'command line interface demonstration' 
http://www.umass.edu/microbio/chime/chimehow/fs_cmdln.htm
fails to work in Nav4.04 but works in Nav4.01.

Maybe soon I'll fix it, or maybe Nav4.05 will fix it ....
In any case, these absolute references are probably a good idea.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

Changing the subject to a related issue, I was recently working on a
presentation in which the contents of any one of the three frames I was
using can change.  This created the problem that javascript functions and
variables needed to maintain state disappeared when the frame which defined
them loaded a new document.  After staring at the javascript reference
manual for awhile

http://developer.netscape.com/library/documentation/communicator/jsref/index
.htm

I stumbled upon the following solution.

The javascript functions and variables must be defined in the header of the
frameset!  (Rather than in the header of a particular document to be loaded
into one frame.) Then they remain available regardless of what documents
are in any particular frames.  The minor catch is that you must reference
the variables and functions with absolute references (sound familiar?).
For example, if your javascript contains

var user_option1 = 0;
function apply_options()
{
  // do something controlled by user_option1
}

and that javascript file is included in the header of the FRAMESET file
<script src="my_code.js"></script>

then in any one of the frame documents, you could set user_option1 with

top.user_option1 = 1;

and call apply_options() with

parent.apply_options();

('parent' and 'top' are synonomous as far as I know: top level of the
current window, or parent of the current frame.)

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

        Molmol <molmol-l@mol.biol.ethz.ch>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Molecular Dynamics
Date: Fri, 02 Jan 1998 00:29:16 +0100
To: Rasmol Mailinglist <rasmol@dhcp-srv2.oit.umass.edu>,

Hi all,

for validation of a molecular dynamics approach we need a well known,
small protein molecule which should be available in PDB- or other common
macromolecule-structure-format from both diffraction and NMR-data with
good resolution. NMR-data needs to be in multiple-conformation-format
(PDB: model1, model2, [..]).

We have thought about using Lysozyme because this is one of the best
known proteins. Unfortunately there seems only one entry in the
PDB-archive derived from NMR-data.

We will continue to crosscheck for other entries, but maybe someone has
allready done a similar task and might want to help us!

If someone knows another molecule which might fullfill the requirements
listed above, please email!

Thanks in advance.

------------------------------------------------------------------------
Disclaimer: Due to the fact, that this message will be crossposted to
several groups and lists, I have to write in english (sorry, hope it
does not offend anyone in the local echos).

-- 

Bye,

Marc Saric

Lehrstuhl für Biophysik
Ruhr-Universität Bochum

++++------+------+------+------+------+------+------+------+------+------+
From: Derk Andrew Wierda <dwierda@anselm.edu>
Subject: Re: Chime problem/Navigator 4.03
Date: Fri, 2 Jan 1998 11:12:48 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Hi all,

I tried the page with Netscape 3.02 (gold) and it worked and with 4.03
(pro) and it locked up my Mac.

Hope this helps.

Derk Wierda

>Dear Chimers,
>
>This is a follow up to my previous message about a Chime problem with
>Navigator 4.03.
>
>If you try to open the url from my original message, listed below, you will
>get a "File not found" error message. I think the error message is
>misleading. The page does exist at that address, but the same error that
>causes crashes blocks us from opening it. Another way to see it is to go to
>
>
>http://www.mdli.com/chemscape/chime/chime.html
>
>which loads without problem. Then scroll down to and click on...
>
>>   Sample page - Test your Chime installation with the following sample page
>
>
>That should cause a Netscape crash.
>
>So far two people have responded to my original message & both got the
>error message. It looks like it is a real browser problem and not something
>just in my machine.
>
>Hopefully, MDLI has some advice.
>
>Harry
>
>Previous message:
>
>We have encountered a problem that occurs with Netscape Navigator 4.03 on
>the  Macintosh on pages with multiple Chime models.  We have a page with 16
>models in small windows. When we open it into a Netscape window large
>enough so that all the models can fit, every thing is OK. When we open it
>into a smaller Netscape window, so that one line of models is off the
>screen, Netscape always crashes.
>
>We tested this at the MDL site, by trying to open
>
>http://www.mdli.com/chemscape/example/sample/sample.html
>
>It crashed Netscape every time.
>
>When we were using various Navigator 3.0x browsers this did not happen so
>we suspect that it's something in the newer browser.
>
>Limited testing with a Windows95 machine showed no problems there.
>
>If you have Netscape Navigator 4.03 on a  Macintosh would you test the mdli
>page mentioned above and let us know what happens.
>
>If you're at MDL please let us know what you think.  Should we continue to
>stick with and recommend Navigator 3.0x?
>
>Harry Ungar                            haungar@cruzio.com
>C4: Computers in Chemistry at Cabrillo College
>6500 Soquel Dr.                         Aptos, CA 95003
>408-479-5059
>http://c4.cabrillo.cc.ca.us

_______________________________________________________
Derk Andrew Wierda                              Phone: (603) 641-7148
Department of Chemistry                         Fax:   (603) 641-7116
100 Saint Anselm Drive                          dwierda@anselm.edu
Manchester, New Hampshire  03102-1310

++++------+------+------+------+------+------+------+------+------+------+
From: bryan@mdli.com (Bryan Van Vliet) (by way of Eric Martz <emartz@microbio.umass.edu>)
Subject: Chime(tm) / Chime Pro(tm) 2.0 Beta 2 Now Available
Date: Sat, 03 Jan 1998 21:27:35 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

MDL Information Systems, Inc. has posted Chime 2.0 Beta 2 for Windows 95/NT 
at http://www.mdli.com/download/chime or http://www.mdli.co.uk/download/chime.
Highlights:

+ Printing now works properly from Navigator 3.04. Netscape has told us they
  will fix printing of plug-ins in Communicator 4.05 (not yet available.) We
  are working on printing issues with Internet Explorer. 

+ The Chime installer now registers the required file types so that Internet
  Explorer can access local files.

+ Chime 2.0 Beta 2 can now properly hot-link multiple structures into Sculpt
  to, for example, allow overlay of results from a database search. See 
  http://www.intsim.com/chime.html for more details about Sculpt and the
  Chime integration.

We are working on a Macintosh version of Chime 2.0. We are also planning to
provide an SGI version. We are not planning to port Chime 2.0 to Windows 3.1
for the following reasons: the Windows 3.1 user base is shrinking quickly;
the port to Windows 3.1 is not straightforward due to differences between
32-bit and 16-bit architectures; the web browser support for Windows 3.1 is
"challenging" to say the least; 32-bit Windows is a superior architecture;
and the advent of sub-$1000.00 Pentium machines really does provide a 
reasonable upgrade path to 32-bit technology. 

Please read the Release Notes before downloading Chime 2.0. Once
you have installed Chime 2.0, please try the demonstrations.

Bryan Van Vliet
Director, Internet Technologies
MDL Information Systems, Inc.

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Chime 2 beta 2 is IMPRESSIVE!
Date: Sat, 03 Jan 1998 22:29:23 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

For those who haven't taken a look and are curious, Chime 2 (now available
for beta-test v2 for Win95 only) has some very impressive new features not
mentioned in Bryan van Vliet's announcement which just preceded this message.

Many of these can be seen by viewing the demonstration pages provided at
MDL's site, http://www.mdli.com/download/chime/

Here are some that I especially like.

MENUS are greatly enhanced:

The most dramatic menu change is a new 'Select' menu. It allows selection
by atom, residue, chain, or model (submenus list all present in the loaded
structure!), or selection of protein, dna, backbone, solvent or
non-solvent, ligand, non-hydrogen, or predefined terms such as
'hydrophobic', 'pyrimidine' etc. etc. (all on a menu!). From the Select
menu, you can change a mouse-click from merely identifying an atom to
selecting atoms, bonds, chains, or residues. Moreover, the 'Modify
selection mode' menu allows newly selected items to be added to or
subtracted from the currently selected set (and other Boolean options)!
'Highlight selection' makes all selected atoms orange, so it is easy to see
what you're doing. And there are menu options to 'hide selected' or 'invert
selection'.

Also on the Select menu is a 'Change color to' menu which lists 13 colors
(this list may be expanded in a future release since Chime now recognizes,
at command level, over 100 Navigator color names).

The 'amino' color scheme (always available from the command line) is now on
the Color Menu.  It is preferred by some to the Shapely color scheme which
has always been on the menu.

Edit, Copy Chime Script now places on the clipboard (ready to be saved to a
file e.g. by Wordpad -- as PLAIN TEXT) a RasMol-style script which will
play back to regenerate the image present when it was saved.  This script
is superior to what RasMol 2.6 beta2a will save in several respects (it
remembers the selected subset of atoms, defined tokens, and the center of
rotation, unlike RasMol; and hopefully soon it will fix the non-black
background bug). This script also includes some of the command-language
enhancements which go beyond RasMol.

Combine the powerful select menu, the copy script capability, and the
ability to load any PDB file from your local hard disk (demonstrated at
http://www.umass.edu/microbio/chime/chimehow/fs_cmdl2.htm -- view this with
Navigator 4.01; 4.04 will give you 'too many' harmless but annoying
javascript errors), and we have the tools for building powerful
presentation development interfaces.

No longer does one need the cumbersome dummy frame and 'immediate button'
mechanism to send commands to Chime.  A single line LiveConnect javascript
function now does the trick (demonstrated as 'Javascript to Chime' at MDL's
demo site).

New button types supported in the text surrounding the image: toggle
buttons which stay depressed when on, and radio buttons.

Mind-blowing enhancements to Chime 2's infrastructure now support:

Clickable spectra: click on a peak and see the bonds responsible
highlighted. This was done in collaboration with Robert J. Lancashire (U
West Indies, Jamaica).

In conjunction with a free module from Sculpt, pull on an atom and watch
real-time energy minimization modeling.

Display molecular surfaces with built-in calculations for electrostatic
potential or molecular lipophilicity potential color schemes.

Excellent animation control -- watch the animation of a chemical reaction
at the demo site.

Not only all the above and more, but we now have DOCUMENTATION (at MDL's
site)!

Hooray for MDL! (pardon my enthusiasm)

Hooray for Tim Maffett who is responsible for many of these enhancements,
and who, I greatly regret, is currently recuperating from injuries suffered
recently while snowboarding.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Adrian Lee <alee@chem.utoronto.ca>
Subject: simple problem
Date: Mon, 05 Jan 1998 12:00:08 -0500
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

Happy New Years to Everyone

    The problem is when I try to display ribbons in very large proteins
such as 1mmo.pdb.  If I write a script for the ribbon display, it will
then take a long time to read this script because of the size of the
file.  I by-pass this problem by trying to type "select all" followed by
"ribbon" in the actual script.  The only problem with this is that it
seems to superimpose the ribbon display onto the wireframe display.  If
this problem is not clear, load 1mmo.pdb then type "ribbon" and you will
see what I mean.  Thank you to anyone who replies.

Sincerely
Adrian

Content-disposition: inline
++++------+------+------+------+------+------+------+------+------+------+
From: "Knapp, Dr. Darin" <knapp.ois2@mhs.unc.edu>
Subject: Re: simple problem
Date: Mon, 5 Jan 1998 13:42:02 -0500
To: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu

I am trying to unscubscribe to the rasmol list.  No luck working with the 
automatied service.  Anyone able to help me?  Thanks.
D. Knapp

Content-disposition: inline
++++------+------+------+------+------+------+------+------+------+------+
From: "Knapp, Dr. Darin" <knapp.ois2@mhs.unc.edu>
Subject: <None>
Date: Mon, 5 Jan 1998 13:57:41 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Rasmolers,

I am trying to unscubscribe to the rasmol list.  No luck working with the 

automated service.  Anyone able to help me?  Thanks.
D. Knapp

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: simple problem
Date: Mon, 05 Jan 1998 14:51:17 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Just insert the command 'wireframe off' in your script to get rid of it.

At 12:00 PM 1/5/98 -0500, you wrote:
>Happy New Years to Everyone
>
>    The problem is when I try to display ribbons in very large proteins
>such as 1mmo.pdb.  If I write a script for the ribbon display, it will
>then take a long time to read this script because of the size of the
>file.  I by-pass this problem by trying to type "select all" followed by
>"ribbon" in the actual script.  The only problem with this is that it
>seems to superimpose the ribbon display onto the wireframe display.  If
>this problem is not clear, load 1mmo.pdb then type "ribbon" and you will
>see what I mean.  Thank you to anyone who replies.
>
>Sincerely
>Adrian
>
>
>
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: New PDB Mirror Sites
Date: Thu, 08 Jan 1998 15:12:19 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

This message was sent to the RasMol list on Dec 23 but didn't get broadcast
till now because of a technical failure. -Eric Martz

++++------+------+------+------+------+------+------+------+------+------+
From: "Nancy O. Manning" <oeder@pdb.pdb.bnl.gov>
Date: Tue, 23 Dec 1997

The PDB is very pleased to announce the availability of two new Official
Mirror sites now on-line.  These new sites will help to better serve the
needs of users around the world by maintaining up-to-date copies of the
PDB archives for access via the World Wide Web.

These new mirrors have been established at:

      http://pdb.gmd.de/       The German National Research Center for
      Information Technology (GMD), Sankt Augustin, Germany

      http://pdb.icm.edu.pl/   The Interdisciplinary Centre for
      Mathematical and Computational Modelling (ICM), Warsaw University,
      Poland

These are now available from the PDB WWW Mirror Sites page,
http://www.pdb.bnl.gov/pdb-docs/mirror_sites.html.  On behalf of the
PDB, I would like to welcome them and thank them for offering this
service.

There is now a total of 11 available PDB Mirror Sites:

Cambridge Crystallographic Data Centre, UK
EMBL Outstation, European Bioinformatics Institute, UK
German National Research Center for Information Technology, Germany
Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Brazil
Interdisciplinary Centre for Modelling, Poland
Institute of Physical Chemistry, Peking University, China
National Tsing Hua University, Taiwan
University of Georgia, USA
University of San Luis, Argentina
The Walter and Eliza Hall Institute of Medical Research, Australia
Weizmann Institute of Science, Israel

We thank all of our Mirrors for their efforts in maintaining these as
up-to-date copies of the PDB Web and FTP servers.

-- 
_______________________________________________________________________

 Nancy Oeder Manning                  Protein Data Bank
 Head User Support                    Brookhaven National Laboratory
 oeder@bnl.gov                        Biology Department, Bldg. 463
 (516) 344-5744 phone                 P.O. Box 5000
 (516) 344-5751 FAX                   Upton, NY 11973-5000   USA
_______________________________________________________________________

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Three cheers
Date: Sun, 11 Jan 1998 19:40:51 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

I sent this message on Jan 4 but it didn't get into the history file (I
have no idea why) and may not have been broadcast properly and so I'm
resending it:

In my previous message (Jan 3, "Chime 2 beta 2 is IMPRESSIVE!"), I said
"Hooray for MDL". To place credit where credit is due, I'd like to put in a
word of appreciation for Bryan van Vliet, head of the Chemscape & Chime
development team at MDL.  Bryan has held Chime development and the team
together and on course during a very trying year, through illnesses,
departures of staff, and other crises.  So ... Three Cheers for Bryan!!

(Hope I didn't embarass you Bryan, but it needed to be said!)

-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

X-ZSender: rowland.geoff@zetnet.co.uk
++++------+------+------+------+------+------+------+------+------+------+
From: Geoffrey Rowland <rowland.geoff@zetnet.co.uk>
Subject: Unit Cells and Axes
Date: Thu, 15 Jan 1998 01:59:54 GMT
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: rwland.geoff@zetnet.co.uk

Hello All,

Inspired by the RasMol home page and the many other sites around the 
web, I'm starting to use RasMol/Chime to develop some materials for 
A-level (pre-University) Science students. At the moment I am 
generating .pdb format files for some inorganic structures (elements, 
hydrides, oxides and chlorides). This has largely involved using 
Babel to convert files from CSSR (.xr) to .pdb format. Since it would 
be nice to show the unit cell for some or all of these files, I have 
also text-edited the CRYST1 line into the .pdb files.  CSSR files 
contain the relevant crystallographic information but Babel does not 
convert this.

However, if my understanding is correct, I have encountered a slight 
problem with the 'set axes on' and 'set unitcell on' commands in 
RasMol 2.6b (and hence also Chime?). If the Cartesian axes are 
displayed using 'set axes on' the Y-axis seems to be labelled in the 
negative direction rather than the positive direction. Similarly, at 
least when the unit cell has cubic symmetry (e.g. NaCl), the unit 
cell also seems to be drawn with the b axis pointing in the negative 
direction.  Hence, if the x, y and z atom co-ordinates of a pdb file 
are all positive in value, the unit cell is drawn alongside, rather 
than enclosing, the atom positions.

I would be most grateful if anyone could confirm if there is a 
problem and, assuming there is, suggest any work-around or fix - 
particularly if this does not involve recalculating the positions of 
all the atoms in all the files. Just sticking a minus sign in front 
of the b value of the CRYST1 record seems to work for cubic unit 
cells but I suspect this won't necessarily work for other symmetries. 
My 3-D geometry isn't up to this at the moment!

In scanning previous Rasmol Emails I came across the following 
contribution by Hidehero Uekusa which seems to concern the same problem.

>From: Hidehiro UEKUSA <uekusa@chem.titech.ac.jp>
>Subject: Re: displaying crystals 
>Date: Tue, 04 Feb 1997 11:49:21 +0900
>To: rasmol@noc1.oit.umass.edu

>In my experience in ver. 2.6, angles alpha and beta angle in 'CRYST1'
>line should be 'inverted', i.e., subtracted from 180 degree when
>composing 'CRYST1' line (if beta is 100 degree, enter 80 in the line.
>But this might be my misunderstanding).

Another problem, which may or may not be related to the above, is 
that if the line of a unit cell intersects an atom sphere the correct 
perspective (i.e. whether the line is partially hidden) is not always 
displayed. There seems to be a particular problem if there is an atom 
at the corners of the unit cell. 

Any ideas ?

Many thanks,

Geoff Rowland, Yeovil College

Content-MD5: vfDO/FbLU7MdyAkQ4wtC+A==
++++------+------+------+------+------+------+------+------+------+------+
From: Erik Lindahl <erik@theophys.kth.se>
Subject: remove
Date: Thu, 15 Jan 1998 08:19:58 +0100 (MET)
To: rasmol@dhcp-srv2.oit.umass.edu

> Date: Thu, 15 Jan 1998 01:59:54 GMT
> From: Geoffrey Rowland <rowland.geoff@zetnet.co.uk>
> To: rasmol@dhcp-srv2.oit.umass.edu
> Cc: rwland.geoff@zetnet.co.uk
> Subject: Unit Cells and Axes
> X-ZSender: rowland.geoff@zetnet.co.uk
> X-Listprocessor-Version: 8.1 -- ListProcessor(tm) by CREN
> 
> Hello All,
> 
> Inspired by the RasMol home page and the many other sites around the 
> web, I'm starting to use RasMol/Chime to develop some materials for 
> A-level (pre-University) Science students. At the moment I am 
> generating .pdb format files for some inorganic structures (elements, 
> hydrides, oxides and chlorides). This has largely involved using 
> Babel to convert files from CSSR (.xr) to .pdb format. Since it would 
> be nice to show the unit cell for some or all of these files, I have 
> also text-edited the CRYST1 line into the .pdb files.  CSSR files 
> contain the relevant crystallographic information but Babel does not 
> convert this.
> 
> However, if my understanding is correct, I have encountered a slight 
> problem with the 'set axes on' and 'set unitcell on' commands in 
> RasMol 2.6b (and hence also Chime?). If the Cartesian axes are 
> displayed using 'set axes on' the Y-axis seems to be labelled in the 
> negative direction rather than the positive direction. Similarly, at 
> least when the unit cell has cubic symmetry (e.g. NaCl), the unit 
> cell also seems to be drawn with the b axis pointing in the negative 
> direction.  Hence, if the x, y and z atom co-ordinates of a pdb file 
> are all positive in value, the unit cell is drawn alongside, rather 
> than enclosing, the atom positions.
> 
> I would be most grateful if anyone could confirm if there is a 
> problem and, assuming there is, suggest any work-around or fix - 
> particularly if this does not involve recalculating the positions of 
> all the atoms in all the files. Just sticking a minus sign in front 
> of the b value of the CRYST1 record seems to work for cubic unit 
> cells but I suspect this won't necessarily work for other symmetries. 
> My 3-D geometry isn't up to this at the moment!
> 
> In scanning previous Rasmol Emails I came across the following 
> contribution by Hidehero Uekusa which seems to concern the same problem.
> 
> >From: Hidehiro UEKUSA <uekusa@chem.titech.ac.jp>
> >Subject: Re: displaying crystals 
> >Date: Tue, 04 Feb 1997 11:49:21 +0900
> >To: rasmol@noc1.oit.umass.edu
> 
> >In my experience in ver. 2.6, angles alpha and beta angle in 'CRYST1'
> >line should be 'inverted', i.e., subtracted from 180 degree when
> >composing 'CRYST1' line (if beta is 100 degree, enter 80 in the line.
> >But this might be my misunderstanding).
> 
> 
> Another problem, which may or may not be related to the above, is 
> that if the line of a unit cell intersects an atom sphere the correct 
> perspective (i.e. whether the line is partially hidden) is not always 
> displayed. There seems to be a particular problem if there is an atom 
> at the corners of the unit cell. 
> 
> Any ideas ?
> 
> Many thanks,
> 
> Geoff Rowland, Yeovil College
> 
> 

---------------------------------------------------------------------
Erik Lindahl, PhD Student	erik@theophys.kth.se
Theoretical Physics, Royal Institute of Technology, STOCKHOLM, SWEDEN
Phone: +46 8 7907172     Fax: +46 8 104879

++++------+------+------+------+------+------+------+------+------+------+
From: Tim Maffett <tim@mdli.com>
Subject: Re: Unit Cells and Axes
Date: Thu, 15 Jan 1998 08:25:10 -0800
To: rasmol@dhcp-srv2.oit.umass.edu

  I believe that these two problems have been fixed in the 
Chime 2.0 beta that is now available at www.mdli.com

-tim

At 05:59 PM 1/14/98 -0800, you wrote:
>Hello All,
>
>Inspired by the RasMol home page and the many other sites around the 
>web, I'm starting to use RasMol/Chime to develop some materials for 
>A-level (pre-University) Science students. At the moment I am 
>generating .pdb format files for some inorganic structures (elements, 
>hydrides, oxides and chlorides). This has largely involved using 
>Babel to convert files from CSSR (.xr) to .pdb format. Since it would 
>be nice to show the unit cell for some or all of these files, I have 
>also text-edited the CRYST1 line into the .pdb files.  CSSR files 
>contain the relevant crystallographic information but Babel does not 
>convert this.
>
>However, if my understanding is correct, I have encountered a slight 
>problem with the 'set axes on' and 'set unitcell on' commands in 
>RasMol 2.6b (and hence also Chime?). If the Cartesian axes are 
>displayed using 'set axes on' the Y-axis seems to be labelled in the 
>negative direction rather than the positive direction. Similarly, at 
>least when the unit cell has cubic symmetry (e.g. NaCl), the unit 
>cell also seems to be drawn with the b axis pointing in the negative 
>direction.  Hence, if the x, y and z atom co-ordinates of a pdb file 
>are all positive in value, the unit cell is drawn alongside, rather 
>than enclosing, the atom positions.
>
>I would be most grateful if anyone could confirm if there is a 
>problem and, assuming there is, suggest any work-around or fix - 
>particularly if this does not involve recalculating the positions of 
>all the atoms in all the files. Just sticking a minus sign in front 
>of the b value of the CRYST1 record seems to work for cubic unit 
>cells but I suspect this won't necessarily work for other symmetries. 
>My 3-D geometry isn't up to this at the moment!
>
>In scanning previous Rasmol Emails I came across the following 
>contribution by Hidehero Uekusa which seems to concern the same problem.
>
>>From: Hidehiro UEKUSA <uekusa@chem.titech.ac.jp>
>>Subject: Re: displaying crystals 
>>Date: Tue, 04 Feb 1997 11:49:21 +0900
>>To: rasmol@noc1.oit.umass.edu
>
>>In my experience in ver. 2.6, angles alpha and beta angle in 'CRYST1'
>>line should be 'inverted', i.e., subtracted from 180 degree when
>>composing 'CRYST1' line (if beta is 100 degree, enter 80 in the line.
>>But this might be my misunderstanding).
>
>
>Another problem, which may or may not be related to the above, is 
>that if the line of a unit cell intersects an atom sphere the correct 
>perspective (i.e. whether the line is partially hidden) is not always 
>displayed. There seems to be a particular problem if there is an atom 
>at the corners of the unit cell. 
>
>Any ideas ?
>
>Many thanks,
>
>Geoff Rowland, Yeovil College
>
>
>
>

X-ZSender: rowland.geoff@zetnet.co.uk
++++------+------+------+------+------+------+------+------+------+------+
From: Geoffrey Rowland <rowland.geoff@zetnet.co.uk>
Subject: Re: Unit Cells and Axes
Date: Thu, 15 Jan 1998 22:36:22 GMT
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Tim et al.,

There still appears to be a problem. In my hands, Rasmol 2.6b, Chime 
1.0 and Chime 2.0 beta 2 (which I've just downloaded and installed 
for the second time) all behave in the same way.

In case it sheds any light on the problem, or identifies a flaw in my 
thinking, try the following pdb format file with a single 
body-centered cubic unit cell of sodium atoms.

HEADER    TEST XYZ/UNITCELL
COMPND    SODIUM BODY-CENTERED CUBIC UNIT CELL
CRYST1    4.235    4.235    4.235  90.00  90.00  90.00 I M-3 M
ATOM      1 Na   UNK     1       0.000   0.000   0.000  1.00  0.00 
ATOM      2 Na   UNK     1       2.118   2.118   2.118  1.00  0.00 
ATOM      3 Na   UNK     1       0.000   0.000   4.235  1.00  0.00 
ATOM      4 Na   UNK     1       0.000   4.235   0.000  1.00  0.00 
ATOM      5 Na   UNK     1       0.000   4.235   4.235  1.00  0.00 
ATOM      6 Na   UNK     1       4.235   0.000   0.000  1.00  0.00 
ATOM      7 Na   UNK     1       4.235   0.000   4.235  1.00  0.00 
ATOM      8 Na   UNK     1       4.235   4.235   0.000  1.00  0.00 
ATOM      9 Na   UNK     1       4.235   4.235   4.235  1.00  0.00 
MASTER        0    0    0    0    0    0    0    0    9    0    9    0
END

I would expect the 'set unitcell on' command or script to draw a unit 
cell starting from Na 1 (0,0,0) at the origin and linking the other 7 
Na atoms at the corners. Indeed, this is what happens if you load the 
file into WebLab Viewer Pro and use the 'Tools, 'Crystal Cell' 
options. However Rasmol and Chime draw the unit cell in an 
immediately adjacent position. If you also use the 'set axes on' 
command/script you can see that the Y-axis points in the negative 
direction (towards the unit cell as drawn). If you rotate the 
structure there also appear to be some odd perspective effects where 
the unit cell intersects the atoms at the corners - in ball and stick mode.

I eagerly await Chime 2.0 beta 3, or a brain-transplant, as appropriate :-)

Geoff Rowland, Yeovil College

> The message <3.0.32.19980115082503.00a2dc88@mind.net>
  from  Tim Maffett <tim@mdli.com> contains these words: 

>   I believe that these two problems have been fixed in the 
> Chime 2.0 beta that is now available at www.mdli.com

> -tim

> At 05:59 PM 1/14/98 -0800, you wrote:
> >Hello All,
> >
> >Inspired by the RasMol home page and the many other sites around the 
> >web, I'm starting to use RasMol/Chime to develop some materials for 
> >A-level (pre-University) Science students. At the moment I am 
> >generating .pdb format files for some inorganic structures (elements, 
> >hydrides, oxides and chlorides). This has largely involved using 
> >Babel to convert files from CSSR (.xr) to .pdb format. Since it would 
> >be nice to show the unit cell for some or all of these files, I have 
> >also text-edited the CRYST1 line into the .pdb files.  CSSR files 
> >contain the relevant crystallographic information but Babel does not 
> >convert this.
> >
> >However, if my understanding is correct, I have encountered a slight 
> >problem with the 'set axes on' and 'set unitcell on' commands in 
> >RasMol 2.6b (and hence also Chime?). If the Cartesian axes are 
> >displayed using 'set axes on' the Y-axis seems to be labelled in the 
> >negative direction rather than the positive direction. Similarly, at 
> >least when the unit cell has cubic symmetry (e.g. NaCl), the unit 
> >cell also seems to be drawn with the b axis pointing in the negative 
> >direction.  Hence, if the x, y and z atom co-ordinates of a pdb file 
> >are all positive in value, the unit cell is drawn alongside, rather 
> >than enclosing, the atom positions.
> >
> >I would be most grateful if anyone could confirm if there is a 
> >problem and, assuming there is, suggest any work-around or fix - 
> >particularly if this does not involve recalculating the positions of 
> >all the atoms in all the files. Just sticking a minus sign in front 
> >of the b value of the CRYST1 record seems to work for cubic unit 
> >cells but I suspect this won't necessarily work for other symmetries. 
> >My 3-D geometry isn't up to this at the moment!
> >
> >In scanning previous Rasmol Emails I came across the following 
> >contribution by Hidehero Uekusa which seems to concern the same problem.
> >
> >>From: Hidehiro UEKUSA <uekusa@chem.titech.ac.jp>
> >>Subject: Re: displaying crystals 
> >>Date: Tue, 04 Feb 1997 11:49:21 +0900
> >>To: rasmol@noc1.oit.umass.edu
> >
> >>In my experience in ver. 2.6, angles alpha and beta angle in 'CRYST1'
> >>line should be 'inverted', i.e., subtracted from 180 degree when
> >>composing 'CRYST1' line (if beta is 100 degree, enter 80 in the line.
> >>But this might be my misunderstanding).
> >
> >
> >Another problem, which may or may not be related to the above, is 
> >that if the line of a unit cell intersects an atom sphere the correct 
> >perspective (i.e. whether the line is partially hidden) is not always 
> >displayed. There seems to be a particular problem if there is an atom 
> >at the corners of the unit cell. 
> >
> >Any ideas ?
> >
> >Many thanks,
> >
> >Geoff Rowland, Yeovil College

++++------+------+------+------+------+------+------+------+------+------+
From: "Jason D. Kahn" <kahn@adnadn.umd.edu>
Subject: Text paste into Windows version command window?
Date: Mon, 19 Jan 1998 10:26:35 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Hello,

   I'm using rasmol for presentation of biochemistry course material. 
In the interests of simplicity and of running on old computers I've
steered away from Chime so far.  Also, I'd like  the students to learn
to manipulate structures as well as appreciate them, and rasmol scripts
hide a lot of these nuts and bolts. 
 
   So, the point, I provide text files of rasmol commands which the
students can use to recreate useful views of biomolecules.  On Mac and
Unix systems, the text can be copied/pasted or X-pasted from Netscape
into the command window and everything works.  However, under Windows
3.11 rasmol won't accept the paste.  The method of saving the file as a
script and then playing it back again tends to hide how the program
works and prevents easy stepping through the script.

   Is there any way to paste text into the command window of the Windows
version?  

Jason Kahn
*-  Jason D. Kahn          Department of Chemistry and Biochemistry  -*
*-  (301) 405-0058         University of Maryland                    -*
*-  fax 405-9376           College Park, MD  20742-2021              -*
*-  kahn@adnadn.umd.edu, http://www-chem.umd.edu/biochem/kahn/       -*

References: <34C370AB.41C6@adnadn.umd.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Fernando Augusto Schuh <fschuh@zaz.com.br>
Subject: Re: Text paste into Windows version command window?
Date: Mon, 19 Jan 1998 14:06:40 -0300 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu

I didn't tried, because I only use Rasmol for artwork. But I think in
Windows 95 it will work.

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Chime vs. Navigator 4.04
Date: Sat, 24 Jan 1998 17:53:27 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

On January 1, I described the solution to why many of my Chime resources
(at http://www.umass.edu/microbio/chime/) failed under Navigator 4.04
despite working under Navigator 4.01.

I have now upgraded my resources; I believe nearly all will now work with
Navigator 4.04 and Chime 2 beta 3. The only exception (noted at
http://www.umass.edu/microbio/chime/prereqs.htm) is my protein secondary
sructure tutorial.  I am planning to port this to the format used in my
other recent tutorials (e.g. hemoglobin and antibody) and so am not
upgrading it. It still works with Navigator 3.01 and Chime 1.0.

The new versions are available for download, as always.

Thanks again to Bryan van Vliet for tracking down the solution.

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: 2 long-time Chime/Rasmol frustrations.
Date: Sun, 25 Jan 98 16:31:28 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

Hello, I'm sharing a couple of things that have frustrated me for awhile 
in my work with Chime and Rasmol, in the hopes that some of you have 
found work-arounds for them. In the event that it is significant here (as 
far as different versions of Chime and Rasmol go), I am using a Power Mac 
8500/233, Netscape 3.0x/Chime 1.0, and Rasmol 2.6.

1. Problems using GZipped files

Anyone else find this annoying? In order for Chime to recognize a Gzipped 
.pdb file (for example), it must be renamed from filename.pdb.gz to 
filename.pdb. This is confusing for ftp clients, because it is now a 
binary file, but with an extension that suggests it is a text file 
(.pdb). So if my file-mapping is set to download a .pdb file as text (and 
type it as a Rasmol file), a binary GZipped .pdb will get corrupted if 
downloaded/uploaded. That is, unless I up/download the GZipped files 
separately and specify that they are binary. If you're up/downloading an 
entire site or tutorial at a time this is a hassle and easily forgotten 
if in a hurry. Then suprise, none of the models load, because they are 
all corrupt.

Also, I've seen some strange issues where some Netscape/Chime on some 
Macs and PC's won't recognize Mac-created gzipped pdb files if their file 
type is left GZIP (default for MacGZip). If I change the file type to 
text they work. But then the custom icon that helps you tell the 
difference in directory listings between Gzipped and ordinary pdb files 
is lost. This is useful since Rasmol can't read GZipped pdb files and I 
frequently jumped between Rasmol and Chime when working on tutorials.

It would be nice if Chime could recognize the .gz suffix in order to 
allow dedicated file-mapping for binary vs. text molecule files. Or has 
someone found a good work-around?

2. Chime cartoons vs. Rasmol cartoons; Blocky cartoons vs. smooth 
cartoons.

OK, everyone must have noticed this. There are two different types of 
"cartoon" rendering. The ribbon and sheet structures themselves look 
about the same in both types. The difference is in the segments of 
non-helical or non-sheet residues. In Chime, if you select 
Display->Cartoons from the Chime menu, you get a nice, rounded-smooth 
rendering of these segments. If you tie a Rasmol script containing 
"cartoons true" to a button, you get a much blockier, square rendering. 
Similarly in Rasmol, if you use the command line "cartoons true" you get 
the blockier rendering. If you select Cartoons from the Display pulldown 
menu at the top of the screen, you get the smoother rendering.

Is there any way to get the smoother cartoons rendering in Chime without 
forcing the user to use the Chime menu? I'd really like to use it in some 
of our tutorials, which generally use Rasmol scripts and (when it can't 
be avoided) JavaScript.

thanks,
Slaton Lipscomb

C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

++++------+------+------+------+------+------+------+------+------+------+
From: Bryan Van Vliet <bryan@mdli.com>
Subject: Re: 2 long-time Chime/Rasmol frustrations.
Date: Sun, 25 Jan 1998 22:57:47 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

>Anyone else find this annoying? In order for Chime to recognize a Gzipped 
>.pdb file (for example), it must be renamed from filename.pdb.gz to 
>filename.pdb. 

This is a function of your web server and not Chime. If you define the
mime-type on your web server so that the file extension pdb.gz is mapped
to chemical/x-pdb, then the file will be opened properly by Communicator,
while Navigator 3.04 gives an alert, but then opens it anyway. Defining
a mime type pdb_gz works for both Navigator and Communicator. I haven't
tried Internet Explorer 4.0. 

You're a bit stuck on local files on your personal computer, but there's
not much advantage to having the files compressed on your local hard drive
(other than maintaining parity between your server and your desktop, of
course.)

In my humble opinion it would have been nice if Netscape and Microsoft
and other companies writing web servers automatically handled compressed
files and that we didn't have to do anything to offer this capability.
After all, it seems like it would be useful to more than just a chemical/
biological structure plug-in.

>Also, I've seen some strange issues where some Netscape/Chime on some 
>Macs and PC's won't recognize Mac-created gzipped pdb files if their file 
>type is left GZIP (default for MacGZip). If I change the file type to 
>text they work.

Again, this is totally out of our control. Netscape instantiates our
plug-in, and we are at their mercy. 

>OK, everyone must have noticed this. There are two different types of 
>"cartoon" rendering. The ribbon and sheet structures themselves look 
>about the same in both types. The difference is in the segments of 
>non-helical or non-sheet residues. 

I took a quick look through the code and didn't see anywhere that
we were handling the two cases differently. Generally, our menu
items quickly drop down into the script parser anyway, so you 
shouldn't see differences. The only thing I can think of is that
you are forcing the palette when you go through the menu item and
not when you are going through a script. You can get smoother
output by selecting "Color" "Force Palette" or with the embed tag
option palette=foreground. Note that this sometimes causes display 
anomalies in Navigator/Communicator, since they are very finicky about
only picking from the 218 color palette they use.

If I am missing something, send a test case to "chime-feedback@mdli.com"
and we will look into it.

- Bryan

----------------------------------------------------------------------
| Bryan Van Vliet                                     bryan@mdli.com |
| Director, Internet Technologies         510.895.1313 x1160 (Voice) |
| MDL Information Systems, Inc.                   510.352.2870 (Fax) |
| 14600 Catalina Street, San Leandro, CA 94577   http://www.mdli.com |
----------------------------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Re: 2 long-time Chime/Rasmol frustrations.
Date: Sun, 25 Jan 98 22:51:51 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

Thanks for the tips Bryan regarding configuring a server to map 
filename.pdb.gz to the chemical/x-pdb mime. Why didn't I think of that? 
You also said:

>You're a bit stuck on local files on your personal computer, but there's
>not much advantage to having the files compressed on your local hard drive
>(other than maintaining parity between your server and your desktop, of
>course.)

However I used the same logic as above to configure my client-side 
browser to do the same thing. I just added the extension .pdb.gz to .pdb 
in the Netscape listing for chemical/x-pdb. It works fine for opening 
gzipped local files with the .pdb.gz extension. This is great. Of course 
for anyone to use one of our tutorials locally, they would have to 
configure their own Netscape similarly, but this is a big step in the 
right direction.

Regarding my second question:

>>OK, everyone must have noticed this. There are two different types of 
>>"cartoon" rendering. The ribbon and sheet structures themselves look 
>>about the same in both types. The difference is in the segments of 
>>non-helical or non-sheet residues. 

I may not have been clear enough in my question or perhaps this is a 
platform specific issue (I'm on a Mac). Attached to the end of this email 
is a letter I just sent to chime-feedback@mdli.com as you suggested, 
guiding a user through a specific example of what I'm describing. Sorry 
to everyone else about the length of this post.

thanks,
Slaton Lipsomb

-------------------------

(Letter sent to chime-feedback@mdli.com 1/25/98)

Hello,

This is a follow-up to my post on Eric Martz's Rasmol Email List, 
regarding an irregularity between cartoon renderings in Chime (and 
Rasmol). Bryan Van Vliet suggested that I write in with a "test case". 
Here it is. It is easiest demonstrated in Rasmol, but the exact same 
problem exists in Chime. In case this is a platform-specific issue, I am 
using a Power Mac 8500/233, Chime 1.0, and Netscape 3.0x (NS 4 is still 
weird with Chime 1.0); also Rasmol 2.6.

Do this:

1. Open a protein with Rasmol. Preferably a small one with some helices, 
sheets, and random structure.
2. Using the Colour pulldown menu, select Colour->Structure.
3. Using the Display pulldown menu, select Display->Cartoons.

In this coloring scheme, usually alpha helices will be pink, beta sheets 
will be yellow, and random segments will be white (or blue, not sure how 
Rasmol/Chime decides). Zoom in so that you can clearly see a stretch of 
white random protein. Notice that it has a smooth, rounded appearance.

Now:

1. Go to the command line and type "cartoons true".

Notice that the rounded appearance of the non-helical/sheet protein has 
become blocky and squarish. The helices and sheets look the same, but the 
other segments look quite different.

OK, this is what I was talking about referring to there being two 
different types of cartoon rendering in Chime and Rasmol. You get the 
smooth, rounder appearance in Chime if you use the Chime Menu to select 
Display->Cartoons, just like using the pulldown menu in Rasmol. You get 
the blocky square looking appearance if you use buttons tied to Rasmol 
scripts that use "cartoons true".

I work on tutorials for instructor and student use that make extensive 
use of Chime. We do a lot of Rasmol scripting with buttons and Javascript 
to implement sequential rendering and movement changes in a given 
protein. Admittedly, it's partly an aesthetic issue - I like the look of 
the smooth cartoons better than the blocky ones - but it's also a matter 
of consistency. I'd like what the instructors or students select with the 
Chime menu to look the same as what we show them with Rasmol scripts and 
buttons.

Is there a way to get the smoother-looking cartoons without using the 
Chime Menu?

This is not a Netscape palette issue, since it happens in Rasmol as well 
as Chime. Using the embed option palette=foreground (as suggested) has no 
effect and does not appear to be involved.

Many thanks,
Slaton Lipscomb

C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

        slaton@surfnetusa.com
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: 'Smooth' cartoons by command
Date: Mon, 26 Jan 1998 18:06:53 -0500
To: rasmol@dhcp-srv2.oit.umass.edu, chime-feedback@mdli.com,

Slaton Lipsomb has recently called our attention to the differences in
rendering achieved with Display->Cartoons (from the menu) vs. 'cartoons'
from the command line (in both RasMol and Chime).

I never noticed this before but I can see what he means.  Here is my
diagnosis and a proposed solution:

The Display menu Cartoons is actually generating a hybrid rendering in
which helices and sheets are rendered as solid ribbon cartoons (sheets with
arrowheads), while turns and 'other' (blue and white in the secondary
structure color scheme) are rendered as 'traces' (a smooth spline trace of
the backbone alpha carbons).  The 'cartoon' command renders everything in
cartoon format: the helices and sheets are the same, but the turns and
other are a square cylinder cartoon instead of a rounded cylindrical one.

It appears to me that you can achieve the result of the menu with the
following set of commands (which could be saved in a script file named
cartoonm.spt [m for menu]).

define temp selected
select not (helix or sheet)
trace 0.4
select temp

Explanation: the first and last lines preserve whatever was the selected
subset when cartoonm.spt was called.  The 'select not ...' command selects
the blue and white regions, and the trace command changes the rendering of
these, leaving the helices and sheets as cartoons. By default, the 'trace'
command seems to give a cylinder radius of 0.33 Angstroms, whereas the
display menu cartoons uses about 0.4 Angstroms.

A reminder concerning secondary structure may be in order.  If helix,
sheet, and turn records are present in the PDB file, RasMol/Chime obey them
regarding the secondary structure colors, and the helix and sheet select
commands.  If the records are absent, RasMol makes its own determination
(which usually differs slightly).  If the records are present, you can
force the application of RasMol's internal rules with the command
'structure'. When you first apply 'color structure' (from either the menu
or the command line), if there is no report of the counts of helices,
sheets, and turns, then records were present in the PDB file; if there is a
report, the records were absent.  The report is from the application of
RasMol's internal rules.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Re: 'Smooth' cartoons by command
Date: Mon, 26 Jan 98 21:15:59 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

Eric Martz wrote:

>The Display menu Cartoons is actually generating a hybrid rendering in
>which helices and sheets are rendered as solid ribbon cartoons (sheets with
>arrowheads), while turns and 'other' (blue and white in the secondary
>structure color scheme) are rendered as 'traces' (a smooth spline trace of
>the backbone alpha carbons).  The 'cartoon' command renders everything in
>cartoon format: the helices and sheets are the same, but the turns and
>other are a square cylinder cartoon instead of a rounded cylindrical one.
>
>It appears to me that you can achieve the result of the menu with the
>following set of commands (which could be saved in a script file named
>cartoonm.spt [m for menu]).
>
>define temp selected
>select not (helix or sheet)
>trace 0.4
>select temp

Excellent! Thank you Eric, this is exactly what I was looking for. I 
tried it out and it looks exactly the same. I wonder how it came to be in 
the first place that Rasmol's Display menu Cartoons uses this "hybrid 
rendering". It also makes me wonder if this is how Chime parses the Chime 
Menu Display->Cartoons command.

>A reminder concerning secondary structure may be in order.  If helix,
>sheet, and turn records are present in the PDB file, RasMol/Chime obey them
>regarding the secondary structure colors, and the helix and sheet select
>commands.  If the records are absent, RasMol makes its own determination
>(which usually differs slightly).  If the records are present, you can
>force the application of RasMol's internal rules with the command
>'structure'. When you first apply 'color structure' (from either the menu
>or the command line), if there is no report of the counts of helices,
>sheets, and turns, then records were present in the PDB file; if there is a
>report, the records were absent.  The report is from the application of
>RasMol's internal rules.

Thanks for the Rasmol lesson. Much appreciated.

regards,
Slaton Lipscomb

C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

++++------+------+------+------+------+------+------+------+------+------+
From: Timothy Driscoll <tdriscoll@amherst.edu>
Subject: connect records - poof!
Date: Thu, 29 Jan 1998 14:32:04 -0500
To: Rasmol <rasmol@dhcp-srv2.oit.umass.edu>

I recently modified a structure within Rasmol, then saved it as a new
pdb file using the Rasmol menu.  When I opened the new pdb in a text
editor, I noticed that all of the connect records were gone.  I didn't
notice anything different about the structure when I opened it in Rasmol
again, though - I could zoom, rotate, ID atoms, etc.

Has anyone else experienced this phenomenon?  Could I be in trouble with
more complex commands?

Thanks,

Tim

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: connect records - poof!
Date: Thu, 29 Jan 1998 16:03:36 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

I believe RasMol determines ALL bonds dynamically based on elements and
distances, unless CONECT records are present for EVERY bond (rarely the
case for macromolecule PDB files).  The only exception I know about is that
if there are CONECT records only for double bonds, it will obey these (see
http://www.umass.edu/microbio/rasmol/faq_em.htm#doublebonds for a details
and an example).

N.B. that RasMol does not determine hydrogen bonds dynamically -- for these
it uses simple (and sometimes wrong) rules for backbones and base pairs
only.  It cannot show Hbonds for nonbackbone, e.g. between proteins or
sidechains.

Both for saving subsets of atoms from PDB files and for dynamic Hbond
determination, much better to use SwissPDBViewer than RasMol. It is also
free and cross-platform. http://www.expasy.ch/spdbv/mainpage.htm

Some of the differences in saving PDB files were documented recently
at http://www.umass.edu/microbio/rasmol/pdbtools.htm, but I left out CONECT
records.

Nicolas Guex (author of SwissPDBViewer): does your program discard CONECT
records?

We probably need Roger Sayle to give us an authoritative rundown on whether
RasMol ever saves CONECT records. It would be good to get this documented
in the manual (which currently it is not).

At 02:32 PM 1/29/98 -0500, you wrote:
>I recently modified a structure within Rasmol, then saved it as a new
>pdb file using the Rasmol menu.  When I opened the new pdb in a text
>editor, I noticed that all of the connect records were gone.  I didn't
>notice anything different about the structure when I opened it in Rasmol
>again, though - I could zoom, rotate, ID atoms, etc.
>
>Has anyone else experienced this phenomenon?  Could I be in trouble with
>more complex commands?
>
>Thanks,
>
>Tim
>
>
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: reply to fax
Date: Thu, 29 Jan 1998 17:26:03 -0500
To: drbob@uccaribe.edu (Dr. Robert Villafane )
Cc: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu

At 11:33 PM 1/27/98 -0400, you wrote:
> While I have your attention, a quick Rasmol
>question, how do I determine what a hetero molecule is called in order to
>do a restrict function on it? I work with the P22 phage tailspike protein
>and it is an LPS-binding protein. There
>available an x-ray structure of it in complex with its substrate LPS (1TYU,
>1TYW, 1TYX, 1TSP). I can not tell which name to use for the LPS to do a
>restrict. Would it be possible for you to tell me how to do it? Thanks. 
>   with high hopes,      Bob  Robert Villafane Ph.D. 
>Assoc Prof of Microbiology 
>UCC Sch Med, Puerto Rico

I took a look at 1tyu.  The only thing other than protein and water is an
octasaccharide.  There are several ways to restrict to it.

1. 'restrict ligand' works fine.  'ligand' is defined as 'hetero and not
solvent' by RasMol. (See the manual at
http://www.umass.edu/microbio/rasmol/distrib/rasman.htm)

2. Examine the PDB file and note that the residues are designated GAL, MAN,
TYV, RAM. 'restrict (gal or man or tyv or ram)'.  Unfortunately RasMol has
no predefined set term such as 'sugar' or 'carbohydrate'. (See the manual)

3. Inspect the PDB file and if the desired residues have a separate chain
designation from the protein, such as chain S for sugar, 'select :s', but
in this case there are NO chain designations in the PDB file.  (You could
use my NEWCHAIN.EXE program to add them but it would require cutting and
pasting different parts of the PDB to get different chain letters, as my
program is rudimentary and puts a single chain letter onto all ATOM records
in the file it is given.) My program is at
http://www.umass.edu/microbio/rasmol/pdbtools.htm#martz

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: gilkes@unixg.ubc.ca (Neil Gilkes)
Subject: chime templates
Date: Thu, 29 Jan 1998 14:51:58 -0800
To: rasmol@dhcp-srv2.oit.umass.edu

I am having trouble using the U. Mass.chime template (Gal4 transcriptional
regulator). When I open twoframe.htm in the Netscape browser (either
Netscape v.3 or v.4), the left frame displays a broken plug-in icon. When I
pass over the frame with the cursor I get the following message at the
bottom of the window:

cgi.netscape.com/eng/mozilla/2.0/extensions/plugin.cgi?application/x-unknown
-content-type

The same thing happens when I load 2FRMCONT.HTM from the chime antibody
template folder.
The U. Mass. antibody presentation works fine when accessed over the Web.
Does anyone have any suggestions. Thanks.

Neil R. Gilkes
Department of Microbiology and Immunology
University of British Columbia
6174 University Boulevard
Vancouver, B.C., CANADA  V6T 1Z3
Tel: (604) 822 6845
Fax: (604) 822 6041

++++------+------+------+------+------+------+------+------+------+------+
From: "Naomi S. Boxall" <Naomi.Boxall.1@uni.massey.ac.nz>
Subject: A-DNA
Date: Tue, 3 Feb 1998 10:19:14 +1300
To: rasmol@dhcp-srv2.oit.umass.edu

Hi

Does anyone know where I would be likely to find a pdb file on A-DNA?  If
not a pdb file, what could I use instead?

Thanks in advance...

++++------+------+------+------+------+------+------+------+------+------+
From: Tim Hubbard <th@sanger.ac.uk>
Subject: Re: A-DNA
Date: Mon, 2 Feb 1998 22:13:35 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Naomi,

>Does anyone know where I would be likely to find a pdb file on A-DNA?  If
>not a pdb file, what could I use instead?

Structures of A-form DNA in PDB are incidentally (though incompletely)
classified in scop (structural classification of proteins database)
although its main job is protein classification not DNA.  It can be found
at:

http://scop.mrc-lmb.cam.ac.uk/scop/

and at mirrors around the world.

Tim Hubbard

----------------------------------------------------------------------------
Dr Tim Hubbard                         email: th@sanger.ac.uk
Head, Human Genome Analysis            Tel (direct): +44 1223 494983
Sanger Centre                          Tel (switch): +44 1223 834244
Wellcome Trust Genome Campus, Hinxton  Fax: +44 1223 494919
Cambridgeshire. CB10 1SA. UK.          URL: http://www.sanger.ac.uk/Users/th
----------------------------------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: "Dr. Don Harden" <chedbh@panther.Gsu.EDU>
Subject: Re: A-DNA
Date: Mon, 2 Feb 1998 17:20:14 -0500 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu

Naomi,
        You (and anyone else) are welcome to use any graphics or PDB
files on our "PDB FILES FOR TEACHING BIOCHEMISTRY" web site: 

        http://heme.Gsu.EDU/glactone/PDB/pdb.html

The A-DNA is in the Nucleic Acids section.  It is a theoretical model. 

If you want a PDB of a "real" A-DNA your best bet is the Nucleic Acid
Database Project at Rutgers University (http://ndbserver.rutgers.edu), 
[assuming the PDB (http://www.pdb.bnl.gov/) doesn't have what you want]

		
If you are looking for PDBs at the undergraduate biochem level, we have
many proteins (at http://heme.Gsu.EDU/glactone/PDB/pdb.html) divided
into the following categories: 

    Classic Proteins: 12 classical proteins often studied in
        Biochemistry

     Nucleic Acid Binding Proteins: Eight common nucleic acid binding
        proteins

     Krebs Cycle: most of the enzymes involved in the citric acid cycle

     Gluconeogenesis and Glycolysis: most of the enzymes involved in
        gluconeogenesis and glycolysis

     Photosynthesis: many of enzymes the involved in photosynthesis

Good hunting,
Don

On Tue, 3 Feb 1998, Naomi S. Boxall wrote:

> Date: Tue, 3 Feb 1998 10:19:14 +1300
> From: "Naomi S. Boxall" <Naomi.Boxall.1@uni.massey.ac.nz>
> Reply-To: rasmol@lists.umass.edu
> To: rasmol@dhcp-srv2.oit.umass.edu
> Subject: A-DNA
> 
> Hi
> 
> Does anyone know where I would be likely to find a pdb file on A-DNA?  If
> not a pdb file, what could I use instead?
> 
> Thanks in advance...
> 
> 
> 

----------------------------------------------------
Dr. Don Harden   	         don-harden@Gsu.EDU
Department of Chemistry
Georgia State University         ph:  (404) 651-3580
Atlanta, Ga. 30303               fax: (404) 651-1416
http://heme.Gsu.EDU/glactone

X-pmrqc: 1
++++------+------+------+------+------+------+------+------+------+------+
From: "Phyllis Dewar" <DEWARP@micah.chowan.edu>
Subject: Re: A-DNA
Date: Mon, 2 Feb 1998 20:14:47 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Naomi,

A-DNA, B-DNA and Z-DNA an be found at
http://heme.Gsu.EDU/glactone/PDB/DNA_RNA/dna.html

Phyllis

> Date:          Tue, 3 Feb 1998 10:19:14 +1300
> Reply-to:      rasmol@lists.umass.edu
> From:          "Naomi S. Boxall" <Naomi.Boxall.1@uni.massey.ac.nz>
> To:            rasmol@dhcp-srv2.oit.umass.edu
> Subject:       A-DNA

> Hi
> 
> Does anyone know where I would be likely to find a pdb file on A-DNA?  If
> not a pdb file, what could I use instead?
> 
> Thanks in advance...
> 
> 
> 
Phyllis D. Dewar
Department of Science
Chowan College
Murfreesboro, NC 27855
Voice: 919.398.6217
FAX: 919.398.1362

++++------+------+------+------+------+------+------+------+------+------+
From: "J.Lin" <jhlin@iff002.iff.kfa-juelich.de>
Subject: How to save rotated coordinates?
Date: Thu, 5 Feb 1998 11:21:30 +0100 (MET)
To: rasmol@dhcp-srv2.oit.umass.edu

Dear all,

In fact, I have two questions. The first one is: when
I rotate one molecule with RasMol, I want to save 
the current coordinates into a new PDB file, so that
next time when I load this new PDB file, I can see
the orientation I want. It would be also very nice 
if I can also set the center of the screen as the
origin of my new PDB file. If these can be achieved,
then I could combine several PDB files into one file.
Can anybody give me some hints?

The second questions is: in viewing the structure of
a protein or peptide, it would be very nice to see
the relation between the backbone and the side chains.
I wonder if it's possible to see backbone and side
chains ( maybe presented by big balls ) simultaneously
by RasMol.

Any reply is gratefully acknowledged!

Best regards, 

Jung-hsin Lin
-- 
--------------------------------------------------------------------------------
Jung-hsing Lin 
Forum Modellierung und Institut fuer Festkoerperforschung 
Forschungszentrum Juelich GmbH. D-52425 Juelich. Germany 
Phone (Office): +49-2461-61-2515; Fax: - 2983; email: j.lin@fz-juelich.de   
Phone/Fax (Home): +49-2461-54419; 
Addr:  Muenchener Str. 5, D-52428 Juelich, Germany
------------------------------------------------------------------------------

References: <05180036002142@surfnetusa.com>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: How to save rotated coordinates?
Date: Thu, 05 Feb 1998 12:16:21 -0500
To: J.Lin@fz-juelich.de
Cc: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu

At 11:21 AM 2/5/98 +0100, you wrote:
>In fact, I have two questions. The first one is: when
>I rotate one molecule with RasMol, I want to save 
>the current coordinates into a new PDB file, so that
>next time when I load this new PDB file, I can see
>the orientation I want. It would be also very nice 
>if I can also set the center of the screen as the
>origin of my new PDB file. If these can be achieved,
>then I could combine several PDB files into one file.
>Can anybody give me some hints?

Neither RasMol nor Chime can save rotated coordinates or centers, but
SwissPDBViewer (also free, also Mac or Windows) can.  Details are at

http://www.umass.edu/microbio/rasmol/pdbtools.htm

>The second questions is: in viewing the structure of
>a protein or peptide, it would be very nice to see
>the relation between the backbone and the side chains.
>I wonder if it's possible to see backbone and side
>chains ( maybe presented by big balls ) simultaneously
>by RasMol.
>
>Jung-hsin Lin
>Forum Modellierung und Institut fuer Festkoerperforschung 
>Forschungszentrum Juelich GmbH. D-52425 Juelich. Germany

When you select a rendering (backbone or ball-and-stick for example) from
the Display MENU, other renderings for the selected atoms are turned off.
In contrast, when you apply renderings from the command line, other
renderings remain on.  So, for example, with all atoms selected, you can
show both the backbone and the sidechains with:

backbone 0.5
# The next two commands are equivalent to the Display Menu's
# 'Ball and stick' rendering.
wireframe 0.15
spacefill 0.48

There are predefined sets which can be used to 'select backbone' (alpha
carbons) or 'select sidechain' if you wish, before applying renderings.

You suggest that sidechains might be displayed as 'big balls'. I'm not sure
what is the best way to do this and perhaps others can make suggestions.
Here is what first comes to mind.  You can select all the beta carbons and
spacefill them as big as you want.  For example,

backbone 0.5
select *.cb
spacefill 1.5

This would show all sidechains except glycine.  Since X-ray diffraction
crystal-derived PDB's lack hydrogens (unless they have been modeled in),
you won't usually be able to display those.

Have fun, -Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: "Nancy O. Manning" <oeder@pdb.pdb.bnl.gov>
Subject: multimedia projector
Date: Thu, 5 Feb 1998 12:31:16 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

List Members,

We are looking for a good quality, high resolution computer-screen projection
system. Preferably one that can connect to Macs, PCs, and SGIs, and be fairly
portable.  Can anyone point me to a good system?

Thank you very much.

Regards,
Nancy

-- 
_______________________________________________________________________

 Nancy Oeder Manning                  Protein Data Bank
 Head User Support                    Brookhaven National Laboratory
 oeder@bnl.gov                        Biology Department, Bldg. 463
 (516) 344-5744 phone                 P.O. Box 5000
 (516) 344-5751 FAX                   Upton, NY 11973-5000   USA
_______________________________________________________________________

++++------+------+------+------+------+------+------+------+------+------+
From: "J.Lin" <jhlin@iff002.iff.kfa-juelich.de>
Subject: Re: How to save rotated coordinates?
Date: Thu, 5 Feb 1998 19:31:39 +0100 (MET)
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Eric,

Thank you very much for your detailed reply.

> 
> >if I can also set the center of the screen as the
> >origin of my new PDB file. If these can be achieved,
> >then I could combine several PDB files into one file.
> >Can anybody give me some hints?
> 
> Neither RasMol nor Chime can save rotated coordinates or centers, but
> SwissPDBViewer (also free, also Mac or Windows) can.  Details are at
> 
> http://www.umass.edu/microbio/rasmol/pdbtools.htm
> 

  It's really a pity that SwissPDBViewer is only implemented on Mac or
  PC, whereas I use a DEC alpha. It seems that I have to manipulate 
  these coordinates by, say, awk. 

Best regards,

Jung-hsin

-- 
--------------------------------------------------------------------------------
Jung-hsing Lin 
Forum Modellierung und Institut fuer Festkoerperforschung 
Forschungszentrum Juelich GmbH. D-52425 Juelich. Germany 
Phone (Office): +49-2461-61-2515; Fax: - 2983; email: j.lin@fz-juelich.de   
Phone/Fax (Home): +49-2461-54419; 
Addr:  Muenchener Str. 5, D-52428 Juelich, Germany
------------------------------------------------------------------------------

References: <9802051831.AA26206@iff002>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: How to save rotated coordinates?
Date: Thu, 05 Feb 1998 22:39:21 +0100
To: J.Lin@fz-juelich.de
Cc: rasmol@dhcp-srv2.oit.umass.edu

J.Lin wrote:
> 
>   It's really a pity that SwissPDBViewer is only implemented on Mac or
>   PC, whereas I use a DEC alpha. It seems that I have to manipulate
>   these coordinates by, say, awk.
What OS are you running?? UNIX (DEC/OSF ??) or NT? If you are using NT,
there is an excellent emulator from DEC (called fx32!) which should
enable your system to run Intel 32bit-code.

I should also draw your attention towards Molmol, a free molecular
modelling program developed at ETH Zürich. It might be able to do what
you want. And it is available for almost every system running UNIX and
NT/Win95 (no Mac). In case that it does not work for the DEC, you can
download the sources and recompile it by yourself.

For more information see

http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

-- 

Bye,

Marc Saric

Visit http://www.rat.de/marc_saric/

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++++------+------+------+------+------+------+------+------+------+------+
From: Scot Wherland <scot_wherland@wsu.edu>
Subject: Chime/Helpers
Date: Thu, 5 Feb 1998 16:46:08 -0800 (PST)
To: rasmol@dhcp-srv2.oit.umass.edu

I have set up a web page (http://www.wsu.edu/~wherland/)with a collection of
molecules taken from crystal structures. The purpose is for students to be
able to view and measure experimental structures and compare the parameters
to those predicted by tables of radii, shape predictions models, etc. I also
use Chime for another feature of the page (a periodic table of radii). In
order to keep the two types of structure files distinct I used the WebLab
viewer and their file format (msv) for the crystal structure data and stayed
with pdb for the Chime files. On the PC this worked. However, Mac users do
not have the option of using WebLab viewer, and the UCB extension to RasMol
allows measurement of structures, so this seemed like an answer. I converted
about 200 files to to a format readable by RasMol(UCB) (MDL mol files). That
is the end of what worked. Without changing anything, these mol files will
come up in Chime (1.0) for viewing. In order to measure them I need to force
mol files to be viewed with RasMol(UCB) as a helper. On the Mac using
Netscape 4.04 this is apparently possible
(Edit/preferences/navigator/applications...), but although the helper
(RasMol) comes up, it does not show the file. Trying to manually load the
file that was downloaded also fails (only Chime shows it). On the PC I
cannot edit the preferences to change to a helper for mol files, but on the
PC I do not really need it. 

Any help is appreciated.

Scot
Scot Wherland		        Voice: 509-335-3360
Prof. of Chemistry		FAX: 509-335-8867
Dept. of Chemistry		Email: scot_wherland@wsu.edu
Washington State University
Pullman, WA 99164-4630 USA

++++------+------+------+------+------+------+------+------+------+------+
From: Andy Bates <bates@liverpool.ac.uk>
Subject: Re: multimedia projector
Date: Fri, 6 Feb 1998 09:16:25 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

>List Members,
>
>We are looking for a good quality, high resolution computer-screen projection
>system. Preferably one that can connect to Macs, PCs, and SGIs, and be fairly
>portable.  Can anyone point me to a good system?
>
>Thank you very much.
>

Nancy and everyone,

We have an InFocus LitePro 720, which we like a lot.  It's relatively light
(about 12 lb), and hence fairly portable, even in a hard case, it's bright
- pretty well as good as a regular slide projector, and the connections to
Macs and PCs are very easy, since it has a neat cabling system which revels
either Mac or PC connections by rotating a ring (inevitably, it's called a
Cable Wizard :-).  I have never connected to an SGI machine, but since the
projector can take just about any kind of video input (and adjust itself to
the relevant resolution more or less automatically), then I'm sure it
should be no problem.

The LCD screen at the heart of it has 800x600 pixels; you can of course
project 640 x 480 as a smaller image, but other resolutions are accomodated
by compression, which is ok, but not as clean as 1:1 correspondence between
input and output resolution.

I'm sure you can now get larger resolution machines these days (at a price)
but 800X600 is good enough for our applications.

If you want to project over a large distance, then you would need an
optional long focus lens (The standard one zooms over a small range, so you
can optimise the image size).

It cost us (in the UK) around 7500 sterling, including the case, an
extension to the cable system, and a couple of spare lamps.

All in all, this had slightly less features than some others, but scored
very highly on ease of use, which for us with multiple users was highly
significant.  It really is plug and play with a PC or Mac.

Standard disclaimer - I have no connection with LitePro or their
distributors...

Cheers,

Andy.

__________________
Dr Andrew D. Bates  School of Biological Sciences   University of Liverpool
		    Life Sciences Building   Crown Steet
		    Liverpool   L69 7ZB   UK
Tel-(+44) (0)151 794 4322  Fax-(+44) (0)151 794 4349  Email-bates@liv.ac.uk
http://www.liv.ac.uk/biolsci/html/gsrg_staff_0.html

++++------+------+------+------+------+------+------+------+------+------+
From: Fergus Doherty <mbxfd@unix.ccc.nottingham.ac.uk>
Subject: Re: Chime/Helpers
Date: Fri, 6 Feb 1998 10:11:26 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

>I have set up a web page (http://www.wsu.edu/~wherland/)with a collection of
>molecules taken from crystal structures. The purpose is for students to be
>able to view and measure experimental structures and compare the parameters
>to those predicted by tables of radii, shape predictions models, etc. I also
>use Chime for another feature of the page (a periodic table of radii). In
>order to keep the two types of structure files distinct I used the WebLab
>viewer and their file format (msv) for the crystal structure data and stayed
>with pdb for the Chime files. On the PC this worked. However, Mac users do
>not have the option of using WebLab viewer,

Why not?  I have a copy of it (WebLab viewer) on my Mac?

_____________________________________________________________________
Fergus Doherty PhD,
Molecular and Cell Biology Section,
D Floor,
School of BioMedical Sciences,
University Medical School,
Queen's Medical Centre,
Nottingham NG7 2UH

mailto:Fergus.Doherty@nottingham.ac.uk
Tel:     0115 970 9366
FAX:     0115 942 2225
URL: http://www.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html
Teaching URL: http://www.nottingham.ac.uk/~mbzmail/students/student.html 

        "Re: multimedia projector" (Feb  6,  9:16am)
References: <v03102800b100823f8ce4@[138.253.30.18]>
++++------+------+------+------+------+------+------+------+------+------+
From: "Dawei Lin" <lin@pdb.pdb.bnl.gov>
Date: Fri, 6 Feb 1998 09:44:16 -0500
To: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu

Dear Macromolecular Structure funs,
 Please see the note from Guy Riddihough. You can also find some
discussion are going on the PDB listserver(http://www.pdb.bnl.gov).

----------------------------------------------------------------------
In light of the various ongoing discussions of the one year hold for
structure coordinates, we are hosting a vote on the matter on the
Nature Structural Biology web site, based on a petition to the IUCr
proposed by Alex Wlodawer. I know that the journals Science and
Nature, the IUCr, the PDB and the NIH are interested in the results we
will obtain so potentially, the data may be of some importance in
guiding discussions of future policy.

For the vote to best represent the feelings in and beyond the
structure community it is vital that as many people vote as possible.
Thus I am e-mailing you to ask if you, and your colleagues, would be
interested in contributing your opinions on the matter. The URL for
the site of the vote is:

http://us.nature.com/survey/nsb_poll.nclk

I would not object if you wished to forward this message on to other
colleagues, either structural biologists or scientists with an
interest in the availability of structural data, whom you think may
also want to express their opinion on the matter.

If you have any questions regarding this or any other matter, please
don't hesitate to contact me at this address or tel: 212 726 9313,
fax: 212 679 0735.

Sincerely

Guy Riddihough
Editor, Nature Structural Biology--

-- 

 
--------< *** Dr. Dawei LIN *** >---------------
              Protein Data Bank
             Biology Department  
        Brookhaven National Laboratory   
             Upton, NY 11973
                  U.S.A
        Telepone: 516-344-6359 (office)
             Fax: 516-344-5751
         Email: lin@bnl.gov
------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: Scot Wherland <scot_wherland@wsu.edu>
Subject: Re: Chime/Helpers
Date: Fri, 6 Feb 1998 11:38:13 -0800 (PST)
To: rasmol@dhcp-srv2.oit.umass.edu

Big oops! (and a lot of somewhat wasted effort). There certainly is a WebLab
Viewer Lite (free) for the Mac and it works just fine. The full WebLab
product is the one that is not currently available for the Mac. I will leave
the mol files on the site for those who just want to look at the molecules
quickly (Chime comes up quickly) and to provide ascii files. 
The other process still should have worked, and there are advantages to
measuring the structures with RasMol(UCB)(as well as different advantages
for WebLab), but I am happy to have it work for both communities.
With some emabarassment,
Scot
 
Scot Wherland		        Voice: 509-335-3360
Prof. of Chemistry		FAX: 509-335-8867
Dept. of Chemistry		Email: scot_wherland@wsu.edu
Washington State University
Pullman, WA 99164-4630 USA

++++------+------+------+------+------+------+------+------+------+------+
From: Timothy Driscoll <tdriscoll@amherst.edu>
Subject: [Fwd: Still can't see graphics]
Date: Mon, 09 Feb 1998 12:54:55 -0500
To: Rasmol LIST <rasmol@dhcp-srv2.oit.umass.edu>

This is a multi-part message in MIME format.
--------------83EECCC3F6105E7D5332CF2A

Has anyone else encountered this problem running Chime on Netscape 3.0 on a Macintosh?
--------------83EECCC3F6105E7D5332CF2A
Content-Disposition: inline

Resent-Date: Mon, 9 Feb 1998 12:24:44 -0500 (EST)
Resent-From: <cohlberg@csulb.edu>
Resent-to: tdriscol@unix.amherst.edu
Resent-message-id: <01ITDJHNIC9G8XA55H@amherst.edu>
X-VMS-To: IN%"tdriscoll@amherst.edu"  "Timothy Driscoll"
X-VMS-Cc: IN%"emartz@microbio.umass.edu"
References: <34DE192F.5BBD@csulb.edu> <34DF348A.BF754239@amherst.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: "Jeffrey A. Cohlberg" <cohlberg@csulb.edu>
Subject: Still can't see graphics
Date: Mon, 09 Feb 1998 09:22:22 -0700
To: Timothy Driscoll <tdriscoll@amherst.edu>
Cc: emartz@microbio.umass.edu

Timothy Driscoll wrote:
> 
> Jeff,
> 
> There are other Chime tutorials on Protein Scondary Structure on the Web,
> though they may not be as adaptable as Eric's protsecs.  They can give an idea
> of what is possible in Chime.
> 
> For instance, check out http://www.amherst.edu/~connlab/biochem420.  This is a
> brief broad coverage of the topic, designed for a specific class lecture so
> it's not as user-friendly as others may be (but it's the one that I remember
> off the top of my head!).  There are also a few minor problems that escaped
> initial debugging.  Beyond that, though, this is a good view of how you can do
> simple yet powerful things with Chime.  I can let you have the files for your
> own use if you want; just let me know.
> 
> Good luck!
> 
> Tim

I tried this web site, and once again the graphics didn't show up -- I
got a blank square with the torn page icon in the center.  The same
thing happened when I tried to view the hemoglobin tutorial.  I think I
must be missing some plug-in.  Is there a specific plug-in used to view
the graphics in these files (other than the Chime plug-in), rather than
just the normal Netscape software?  Note: When I follow the link on the
hemoglobin page "How to use Chime", I also get the torn page icons
instead of the three graphics at the top of the page.  I am a relatively
frequent user of the Web, and this is not a universal problem for me --
there are lots of web pages where the graphics come in without a
problem.
		Help!!	Jeff
-- 
Jeffrey A. Cohlberg, Professor
Department of Chemistry and Biochemistry
California State University, Long Beach
1250 Bellflower Blvd.
Long Beach, CA 90840
phone (562) 985-4944	fax (562) 985-8557

--------------83EECCC3F6105E7D5332CF2A--

++++------+------+------+------+------+------+------+------+------+------+
From: "Naomi S. Boxall" <Naomi.Boxall.1@uni.massey.ac.nz>
Subject: Re: [Fwd: Still can't see graphics]
Date: Tue, 10 Feb 1998 10:07:35 +1300
To: rasmol@dhcp-srv2.oit.umass.edu

I'm running exactly the same programs on my macintosh and can see all the
graphics clearly...perhaps something went wrong when you downloaded Chime?
(I'm using Chime 1.0 - not the new version)

Also...I have completed a section of tutorials on biochemistry, and would
appreciate it if some of you could have a quick look at what is there and
let me know your views.  I am pretty sure they won't run too well on IE
(having designed them for NN) but I would like to see/hear what they look
like on the PC platform.

The address is http://www.massey.ac.nz/~wwbioch/Prot/tutehome/tutepage.htm

Thanks in advance...

____________________________________________________________
| Naomi S Boxall BSc		Ph. 064-6-356-9099 ext.4058
|
| Biochemistry Department		Fax. 064-6-350-5688
|
| Massey University		e-mail.  Naomi.Boxall.1@uni.massey.ac.nz |

| Palmerston North
|
| New Zealand							       |
--------------------------------------------------------------------------------
----------------------------------------

References: <l03130300b1051f5bb9c2@[130.123.73.29]>
++++------+------+------+------+------+------+------+------+------+------+
From: Timothy Driscoll <tdriscoll@amherst.edu>
Subject: Re: [Fwd: Still can't see graphics]
Date: Mon, 09 Feb 1998 18:15:03 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

The problem of the busted graphic icon was solved - make sure you leave
Netscape in the same folder as the Plug-ins folder, or none of the Plug-ins
will load (Mac).

Thanks!

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Optimal format for Chime presentations
Date: Tue, 17 Feb 1998 14:09:45 -0500
To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu

This message discusses pros and cons of various Chime presentation
formats, and offers a ready-made template for a new one which combines
several desirable features.

NAVIGATION vs. LEGIBILITY

The first format utilized for Chime presentations had a series of
buttons interspersed in text in one frame, with the Chime graphic in a
second frame. This format was pioneered by Tim Maffett, Henry Rzepa, and
David Marcey to the best of my knowledge.

One disadvantage of the earlier presentations was that the text was
rather small, and hard to read when projected to a group.  In part to
deal with this limitation, I created a new format for linear
presentations, illustrated by my presentation on protein secondary
structure, ProtSecS,
(http://www.umass.edu/microbio/chime/protsecs/index.htm). It has large
text, including a large color key, in a frame at the bottom, and uses
more of the screen for the Chime graphic.

Having observed both formats being projected in large classes, I have
concluded that the navigational control in my ProtSecS format is
inadequate. It is too difficult to jump directly to any desired image,
for example in response to a question, or when the lecturer wishes to
show only a subset of the available images. So while the legend is more
readable from the back of the room, the absence of the button-in-text
map of the presentation (which easily allows hopping about randomly to
any desired image) was too great a sacrifice.

SYNTHESIS: NAVIGATION WITH LEGIBILITY

Recently, in discussion with Tim Driscoll and Rashie Athukorala, we
realized that variable font-size control could be implemented in the
earlier format. I have now done this in the template I provide for
building new presentations, version 2,
(http://www.umass.edu/microbio/chime/prsswc/template.htm) and in our
presentation on Hemoglobin
(http://www.umass.edu/microbio/chime/hemoglob/index.htm).  These two
presentations follow the earlier format (allowing random jumping). Now
you can choose a small font (making it easy to see a whole range of
buttons and the overview of the present topic), or a large font visible
at the rear of a large audience. Font size can be varied at any time,
and remains in effect for all topics in the current session.

Instructions are provided for retrofitting existing Chime presentations
with this font control.  The handful of necessary files can be
downloaded as part of the 'minimal template fileset' needed to build a
new presentation.

TRUE RANDOM ACCESS: INDEPENDENT BUTTONS

While the early format allowed pushing the buttons in any order, most
such presentations on the web are not implemented so as to give the
correct images when this is done.  That is, the scripts attached to
buttons are not independent; many scripts assume that the the previous
button was pushed immediately previously.

One easy way to make scripts which are independent is to save them from
RasMol (or from Chime 2, which has fixed most of the few bugs in
RasMol's script-saving mechanism).  Such scripts always begin with a
fresh start, loading the desired PDB file.  Indeed, if all the scripts
in a Chime presentation are saved from RasMol, one does not need to
learn how to program RasMol/Chime script language.  This is why in my
NSF-supported workshops for faculty
(http://www.umass.edu/microbio/rasmol/workshop.htm), we attach
RasMol-saved scripts to buttons in a pre-existing Chime template. The
template avoids needing to know HTML or javascript. This relatively easy
method of creating a Chime presentation has the large advantage that all
buttons are independent.

Instructions for saving scripts and using the template, complete with
troubleshooting, are available
(http://www.umass.edu/microbio/chime/prsswc/template.htm), and the
template can be downloaded.

It may seem terribly inefficient to reload the PDB file for every button
in a presentation, especially if a very large PDB file is used over and
over. Luckily, IT IS NOT.  First, after the PDB file (hopefully
gzipped!) has been transmitted one time, all subsequent reads are done
from the local cache.  Second, Chime 2, by default, is intelligent
enough to ignore a load command which specifies the same PDB file
already loaded; it just resets everything as though a fresh load had
occurred without actually reloading (thanks to Tim Maffett for
implementing this!).

I am interested to hear the insights and comments of others on these
issues.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: PDB copyrights
Date: Tue, 17 Feb 1998 15:00:30 -0500
To: "Owen Lofthus, II" <olofthus@vt.edu>
Cc: rasmol@dhcp-srv2.oit.umass.edu

At 2/17/98 , Owen W. Lofthus, II wrote:
>Hello,
>
>I am a graduate student at Virginia Tech, and have been put in charge of
>gathering information regarding chime and posting molecules on the web.
>One question which I am unsure if is copyrighting.  If I download a
>molecule from a website, may I post it on mine?  Or do I draw it, then post
>it?  I have already looked over some of your web pages and have learned
>much about CHIME.  If you could lend any advice, it would be greatly
>appreciated.
>
>Thank you,
>
>Owen W. Lofthus, II
>olofthus@vt.edu	
>http://www.vt.edu:10021/O/olofthus/index.html
>Virginia Polytechnic Institute & State University
>Blacksburg, VA  24061

It is my impression that PDB files (atomic coordinate files for
molecules) which are published and publically available from the
Brookhaven Protein Data Bank may be redistributed from another server
(e.g. as part of a Chime presentation), provided the PDB file is
suitably identified, and the authors of the PDB file(s) are suitably
acknowledged in the presentation.

I would appreciate comments from Nancy Oeder-Manning of BNL or others on
this issue.

It is also imperative that MODIFICATIONS to any PDB files be clearly
stated as a remark at the top of the modified PDB file.  I recently
viewed a Chime presentation in which all sidechain atoms had been
deleted from the PDB files, but this was not stated anywhere.  This was
very confusing.  There should at least be a remark at the top of the PDB
file stating what modifications were made to the original, and
preferably the file should be renamed so as not to confuse it with the
original, and of course there should be explicit mention of such
modifications in the presentation text.

If you download something from a private server, you must comply with
the copyright restrictions stated there.  It would also be best to ask
explicit permission to redistribute any information obtained from a
private server.

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <0EOJ00L4NC266W@pobox1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: William R Mcclure <wm0p+@andrew.cmu.edu>
Subject: Re: Optimal format for Chime presentations
Date: Tue, 17 Feb 1998 18:04:28 -0500 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu

Eric,

  Two formats (and some new Chimed topics) that work here are:

1. Tutorial on tRNA, starting at:
http://info.bio.cmu.edu/Courses/BiochemMols/tRNA_Tour/tRNA_Tour.html
(This is a frames format with a selection menu covering several aspects
of tRNA structure.)

2. Molecular Biology Structures, starting at:
http://info.bio.cmu.edu/Courses/BiochemMols/MolBiol/MolBiol.html
(This is a linked-page format that provides a one-page intro to seven
molecules used in our Mol Biol courses.

The second set of pages is converted easily to lecture presentation by
increasing the Chime image to 500x500 from 350x350. Some minor HTML
editing is involved, and two pages are required for each topic, but
everything else is the same on both pages.

-Will McClure 

++++------+------+------+------+------+------+------+------+------+------+
From: "Hidetoshi Kono(Jouhou)'950914" <hkono@rtcmain.rtc.riken.go.jp>
Subject: vectps
Date: Wed, 18 Feb 1998 11:50:59 +0900
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: hkono@rtcmain.rtc.riken.go.jp

Dear all,

I have a question about vectps.
Vectps creates a nice image,
so, I would like to save a stereo image in the vectps format.
But only left hand image are saved.
Is it impossible to save a stereo image using vectps ?
I am using rasmol2.6b2 under IRIS 6.2.

Thanks in advace.

Hidetoshi Kono                                     ---------   __o    
Tsukuba Life Science Center, RIKEN             __________    -\<,
3-1-1 Koyadai, Tsukuba, Ibaraki, 305 Japan            .....  O/ O
hkono@rtc.riken.go.jp Tel:81 298 36 9082 Fax:81 298 36 9080

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: vectps
Date: Wed, 18 Feb 1998 13:50:08 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

The RasMol Manual

http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual

specifically states that stereo is one thing vectps does not support. Stereo was the last feature added to RasMol, and one of the reasons the current version is still a 'beta test' version is that stereo was never fully integrated with other aspects of the program.  Also the manual was never officially updated (the above version is close to up to date, but not done by Roger Sayle), and the on-line help has not been updated since version 2.5.

At 2/18/98 , you wrote:
>Dear all,
>
>I have a question about vectps.
>Vectps creates a nice image,
>so, I would like to save a stereo image in the vectps format.
>But only left hand image are saved.
>Is it impossible to save a stereo image using vectps ?
>I am using rasmol2.6b2 under IRIS 6.2.
>
>Thanks in advace.
>
>Hidetoshi Kono                                     ---------   __o    
>Tsukuba Life Science Center, RIKEN             __________    -\<,
>3-1-1 Koyadai, Tsukuba, Ibaraki, 305 Japan            .....  O/ O
>hkono@rtc.riken.go.jp Tel:81 298 36 9082 Fax:81 298 36 9080
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page http://www.umass.edu/microbio/rasmol
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Win32S: faster RasWin under Windows 3.1
Date: Wed, 18 Feb 1998 18:44:54 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Windows 3.1 users can double the speed of RasMol by using the 32-bit
version of RasWin -- if they have a 386 or better with floating point
hardware (e.g. 387), and if they install a free module called Win32SOle
from Microsoft. On the RasMol Home Page, the link to Win32SOle has been
broken for some time and several people have pointed this out. 
Unfortunately, Microsoft keeps changing the URL and breaking our link. 
Thanks to Rashie Athukorala, the link is fixed again.

More info and the link is on our page at

http://www.umass.edu/microbio/rasmol/getras.htm#raswin

where you will also find instructions on how to install this module.

and the link itself is

ftp://ftp.microsoft.com/softlib/MSLFILES/PW1118.exe

or

http://support.microsoft.com/download/support/mslfiles/Pw1118.exe

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page (http://www.umass.edu/microbio/rasmol)
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: CPK, vectps now in manual
Date: Thu, 19 Feb 1998 19:41:04 -0500
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: wm0p@andrew.cmu.edu, sears@lifesci.ucsb.edu

I have updated the RasMol Manual

http://www.umass.edu/microbio/rasmol/distrib/rasman.htm

to include the complete and correct CPK color scheme as implemented in
RasMol and Chime (taken directly from the source code of RasMol) in
decimal (for RasMol or Chime) and hexadecimal (for Navigator) RGB
values, and also a GIF image showing all 16 colors and the elements they
map to.

If you want to see the GIF image without the RGB data (and the rest of
the 150K manual), go to

http://www.umass.edu/microbio/rasmol/distrib/cpk.gif

I have included some color patches to show colors difficult to
distinguish.  Notably, Zn and Li are only very slightly different; S, P,
and F are similar variants of yellow.

There is also a different GIF image of the CPK color scheme consisting
of bars of color on a white background, suitable for printing ("RasMol's
Flag"?).

http://www.umass.edu/microbio/rasmol/distrib/cpk_barw.gif

Also I noted that 'write vectps' was not mentioned in the manual, and
added it.

It is left as an exercise for the reader to guess why Roger Sayle
assigned a unique color to helium. (If anyone solves this exercise,
please share the solution!)

-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page (http://www.umass.edu/microbio/rasmol)
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: More font size control
Date: Thu, 19 Feb 1998 20:39:26 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

The antibody and MHC Chime presentations at
http://www.umass.edu/microbio/chime/ now have font size control.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page (http://www.umass.edu/microbio/rasmol)
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Baffled by Chime
Date: Wed, 04 Mar 1998 14:10:15 -0500
To: debanzie <debanzie@cherokee.nsuok.edu>
Cc: rasmol@dhcp-srv2.oit.umass.edu

At 3/3/98 , you wrote:
>Dear Dr. Martz,
>
>... with anything [Chime] loaded off my hard drive (your page or a trial
page I
>wrote) I get a message saying that I need a plug-in to deal with a file
>of type "zz-application/zz-winassoc-pdb". Since your site works
>perfectly (nice rotatable molecule) I _know_ I have the plug-in. I have
>also checked the Netscape plug-in info, and the Chime plug-in is in
>there, and is enabled.
>
>What am I missing? Why does my plug-in work for your file on your site,
>but not for your file on my hard drive?
>
>John de Banzie (Assoc. Prof. Biology)
>
>debanzie@cherokee.nsuok.edu

Dear Dr. de Banzie:

You've got me stumped.  I never heard of those zz MIME types before. Is
this with Win95?  Occasionally people have had bizzare problems which went
away when they uninstalled and then reinstalled Navigator and Chime.  That
is all I can suggest.

I assume you're using Navigator's File menu to Open Page (Open in Nav3) the
index.htm file?  Sometimes if people spell out EXACTLY what they are doing
and versions of all software we can spot something you are doing wrong
which we took for granted with a less detailed account.

I've copied this to the rasmol email list in case someone else has seen
these zz MIME types or has a suggestion. (If you don't subscribe, you can
see each day's responses after 3 AM EST the following day at
http://www.umass.edu/microbio/rasmol/raslist.htm)

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page (http://www.umass.edu/microbio/rasmol)
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Chime resources compatible with Nav 3.0x again
Date: Thu, 12 Mar 1998 13:31:18 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

On February 17 and 19, I added font size control to my Chime presentations
on hemoglobin, antibody, and MHC, and to the downloadable template for
making new presentations (http://www.umass.edu/microbio/chime).

Yesterday Tim Driscoll pointed out that these font size controls don't work
properly in Navigator 3.0x and cause it to crash (on both Windows 95 and
Macintosh).  I have therefore disabled font size control when these are
viewed in Nav 3.0x.  All other features work fine in Nav 3.0x, and all
features including font size control work fine in Nav 4.0x. The change is
announced at
http://www.umass.edu/microbio/chime/newchime.htm

Anyone using the template downloaded since Feb 17 may wish to download the
new version and replace the file fontsize.js, which is the only file
changed since then.

Those who built presentations with the template downloaded before Feb 17
can easily install font size control -- instructions are at
http://www.umass.edu/microbio/chime/prsswc/2fc-how.htm

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page (http://www.umass.edu/microbio/rasmol)
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Adrian Lee <alee@chem.utoronto.ca>
Subject: angles
Date: Fri, 13 Mar 1998 13:08:25 -0500
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

Hello Everyone

I was wondering if there are any features of the 2.0 beta is plugin
which allow interactive
viewing of bond angles whereby the angles are displayed directly on the
structure rather than
in a javascript alert box.

Thank you in advance

++++------+------+------+------+------+------+------+------+------+------+
From: Adrian Lee <alee@chem.utoronto.ca>
Subject: Chime 2.0 and button viewing problems with Internet Explorer 4.0
Date: Fri, 13 Mar 1998 15:04:27 -0500
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

    Has anyone had any problems with chime 2.0 and Internet Explorer 4.0
where a page containing embeded chime scripts with buttons do not view
correctly at first but are ok after reloading the page. The problem I am
seeing specfically involves the appearance of phantom buttons when the
page is first loaded. Any help would be greatly appreciated.

++++------+------+------+------+------+------+------+------+------+------+
From: Adrian Lee <alee@chem.utoronto.ca>
Subject: Is there a newsgroup for rasmol and/or chime?
Date: Fri, 13 Mar 1998 15:05:52 -0500
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Chime: IE4, angles, script completion
Date: Fri, 13 Mar 1998 04:21:07 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Adrian Lee asked several questions:

1. QUESTION: IE4

    Has anyone had any problems with chime 2.0 and Internet Explorer 4.0
where a page containing embeded chime scripts with buttons do not view
correctly at first but are ok after reloading the page. The problem I am
seeing specfically involves the appearance of phantom buttons when the
page is first loaded. Any help would be greatly appreciated.

MY REPLY:

I have not heard from anyone at MDL that IE4 is fully compatible with
Chime.  I doubt that it is. Therefore I strongly recommend using Navigator.
 Navigator version 3 is fine with Chime version 1, but if you are using
Chime 2 beta, use Navigator 4.04.

Again, the problem here is not a lack of support for IE from MDL; it is
that Chime is a plugin, Netscape defined the plugin protocol, and IE has
not yet provided full plugin compatibility.

2. QUESTION: ANGLES

I was wondering if there are any features of the 2.0 beta is plugin
which allow interactive
viewing of bond angles whereby the angles are displayed directly on the
structure rather than
in a javascript alert box.

MY REPLY: Not that I know about.  The message call back mechanism allows
you to do something other than put the angle report in a javascript alert
box.  For example you could create a nicely formatted report document in a
separate frame. But I don't think there is any way to get the angle
displayed in the graphic (as there is for distances using the monitor
commands).

3. QUESTION (SCRIPT POPUP)

    The new plugin likes to tell you when a script is completed by
giving you an annoying popup dialogue box. Is there any way around this
other than disabling Javascript? In Internet Explorer 4.0 Javascripts
can not be disabled like they can in Netscape. Does anyone have any
suggestions?

MY REPLY:

I would need to know what url you are looking at. My sites have error
trapping code which puts any unexpected messages in an alert box.  When
Chime 2 beta first  became available, it had additional script completion
messages which caused such alerts.  I believe I have fixed my url's so that
problem is gone.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page (http://www.umass.edu/microbio/rasmol)
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id RAA20073
++++------+------+------+------+------+------+------+------+------+------+
From: Shaun Landau <slandau@alchemy.chem.utoronto.ca>
Subject: Chime pages don't view properly with my Web Server
Date: Fri, 13 Mar 1998 17:47:48 -0500
To: "'Rasmol'" <rasmol@dhcp-srv2.oit.umass.edu>

	I have created some html pages which work fine when accessed by Netscape as local files. I also have a Web server (Microsoft Personal Webserver) running on my machine. When I try to access these same pages via http, i.e. through TCPIP in conjunction with my web server, my Netscape browser seems to not know what to do with the chime graphics even though the plugin has been properly installed. This is clearly not a problem with Netscape but seems to rather be a problem with my server. Are there any settings or extension I must modify on my server in order for people to properly access chime pages? Any insights would be greatly appreciated.

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Chime pages don't view properly with my Web Server
Date: Fri, 13 Mar 1998 05:26:10 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

At 05:47 PM 3/13/98 -0500, you wrote:
>	I have created some html pages which work fine when accessed by Netscape
as local files. I also have a Web server (Microsoft Personal Webserver)
running on my machine. When I try to access these same pages via http, i.e.
through TCPIP in conjunction with my web server, my Netscape browser seems
to not know what to do with the chime graphics even though the plugin has
been properly installed. This is clearly not a problem with Netscape but
seems to rather be a problem with my server. Are there any settings or
extension I must modify on my server in order for people to properly access
chime pages? Any insights would be greatly appreciated.

This is a frequently asked
question. The answer is on Chime's FAQ page at

http://www.mdli.com/chemscape/chime/chimehelp.html#Trouble1

and is also mentioned on my site, e.g. at

Presenting RasMol-Saved Scripts with Chime, then
How to Install Your Scripts into the Chime Template (see last few steps)
http://www.umass.edu/microbio/chime/prsswc/2fc-how.htm
and
Programming Chime web pages from scratch
http://www.umass.edu/microbio/chime/chimehow/chimake.htm

Your server needs to be configured to serve .pdb as chemical/x-pdb, and
.spt as application/x-spt.  If you use any javascript files, also .js as
application/x-javascript.  Otherwise, Navigator doesn't know what to do
with the files (except in local mode).

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page (http://www.umass.edu/microbio/rasmol)
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Shaun Landau <slandau@alchemy.chem.utoronto.ca>
Subject: RE: Chime: IE4, angles, script completion
Date: Fri, 13 Mar 1998 21:55:56 -0500
To: "'rasmol@lists.umass.edu'" <rasmol@dhcp-srv2.oit.umass.edu>

------ =_NextPart_000_01BD4ECA.CE479540

	I am designing my own pages with embedded chime scripts. How did you =
work around the chime 2.0  Javascript alerts and error messages? Is it a =
matter of simply adding some html code to the pages?

-----Original Message-----
Sent:	Friday, March 13, 1998 4:21 AM
From:	Eric Martz [SMTP:emartz@microbio.umass.edu]
Subject:	Chime: IE4, angles, script completion
To:	rasmol@dhcp-srv2.oit.umass.edu

The new plugin likes to tell you when a script is completed by
giving you an annoying popup dialogue box. Is there any way around this
other than disabling Javascript? In Internet Explorer 4.0 Javascripts
can not be disabled like they can in Netscape. Does anyone have any
suggestions?

MY REPLY:

I would need to know what url you are looking at. My sites have error
trapping code which puts any unexpected messages in an alert box.  When
Chime 2 beta first  became available, it had additional script =
completion
messages which caused such alerts.  I believe I have fixed my url's so =
that
problem is gone.


++++------+------+------+------+------+------+------+------+------+------+
From: "Donald W. Low" <dwl@alumni.caltech.edu>
Subject: potential surfaces
Date: Fri, 27 Mar 1998 13:53:15 -0800 (PST)
To: rasmol@dhcp-srv2.oit.umass.edu

Hello all

I tried my best to see if this topic had been covered in the history, so 
forgive me if it has.

The question I have concerns coloring dot surfaces with the gradient color
scheme for electrostatic potential.  I'm using V 2.6 UCB, and I can get my
residues (and their corresponding dots) to be color coded by potential,
but when I try to make the graded potential surface it just ends up giving
me a uniformly red surface.  Any ideas? 

thanks

- Don Low

Gryphon Sciences, USA

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: potential surfaces
Date: Wed, 01 Apr 1998 16:01:30 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

I suggest that you try out Chime 2, which automatically generates solid or
transparent surfaces (not only dot surfaces) and colors them automatically
by electrostatic potential.

www.mdli.com/download/chime

At 3/27/98 , you wrote:
>
>Hello all
>
>I tried my best to see if this topic had been covered in the history, so 
>forgive me if it has.
>
>The question I have concerns coloring dot surfaces with the gradient color
>scheme for electrostatic potential.  I'm using V 2.6 UCB, and I can get my
>residues (and their corresponding dots) to be color coded by potential,
>but when I try to make the graded potential surface it just ends up giving
>me a uniformly red surface.  Any ideas? 
>
>thanks
>
>- Don Low
>
>Gryphon Sciences, USA
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page (http://www.umass.edu/microbio/rasmol)
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Future of RasMol
Date: Sun, 05 Apr 1998 14:26:15 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Rasmolians:

During recent months, you may have noticed the absence, on this email list,
of Roger Sayle's authoritative responses to questions about his creation,
RasMol.  Roger departed from GlaxoWellcome in December, 1997, and is now
residing in the United States, involved in a startup software company.  It
appears unlikely that Roger will make future contributions to RasMol.
Inquiries of the people with whom Roger worked at GlaxoWellcome have
yielded no evidence of plans for further development of RasMol there.

Perhaps volunteers will emerge to improve RasMol, and to compile
executables for Windows95 and Macintosh.  This email list would be an
appropriate medium for coordinating such efforts.  Volunteers to improve
the documentation would also be welcome.  It turns out that Roger had a
sophisticated system for converting the master reference manual into html,
postscript, and the on-line format available from RasMol's Help menu.
Unfortunately, this came to light after Margaret Wong and I had already
updated the html copy to version 2.6.  Were volunteers to emerge, perhaps
the documentation management software could be obtained from Roger and the
html manual restored back to this system.

Is there a need for further development of RasMol?  RasMol is surely in use
by hundreds of thousands of people.  RasMol's unique strengths include its
engaging interface, the high quality and beauty of its renderings, and its
astonishing speed in rotating spacefilled or cartoon images.  On the one
hand, improved versions would likely be used by thousands.  On the other
hand, Chime has inherited nearly all of RasMol's strengths and added many
powerful features.

Chime version one, and especially the html interfaces for it currently on
the web, largely lack the capability for self-directed exploration of any
molecule present on the client's hard disk.  They also lack RasMol's
powerful 'save script' mechanism for playing back carefully constructed
renderings. This is changing.

Chime version two makes possible nearly all of RasMol's strengths in an
even more user-friendly interface, and much more.  Although not yet
released, completion of Chime 2 is receiving intense effort from the staff
at MDL. Loading molecules from the client's hard disk (see example
<www.umass.edu/microbio/chime/chimehow/fs_cmdl2.htm> and saving scripts are
straightforward in Chime 2. Indeed, most of the limitations of scripts
saved by RasMol (see
<www.umass.edu/microbio/chime/prsswc/prssft.htm#forgets>), including the
absolute pathname in the load command which fails when the script is moved,
have been fixed in Chime 2, thanks to the care and attention of Tim Maffett
and Bryan van Vliet of MDL's Chemscape team. New html interfaces need to be
developed before these capabilities are delivered in an optimal way, but
these will likely be forthcoming in the near future. It seems likely that
Chime and these new web interfaces will supercede RasMol for most purposes,
though it will undoubtedly take many years to convert the large established
user-base of RasMol.

Roger's extraordinary generosity in putting RasMol and its source code in
the public domain has borne fruit.  RasMol now has two freeware children
(Chime and Weblab) which incorporate key parts of Roger's brilliant source
code.  There is also one freeware grandchild, a portion of Sculpt bundled
with Chime 2. In closing, since Roger appears to be bowing out, I would
like to thank Roger for his phenomenal contribution to science education
and his years of tireless support of RasMol, and to wish him luck and
happiness in his new ventures.

-Eric 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <0EQY00H1JGRCDW@rfd1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: "Peter C. McCluskey" <pcm@rahul.net>
Subject: DisMol - an applet with many RasMol features (Re: Future of RasMol)
Date: Mon, 6 Apr 1998 09:14:46 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

 emartz@microbio.umass.edu (Eric Martz) writes:
>Roger's extraordinary generosity in putting RasMol and its source code in
>the public domain has borne fruit.  RasMol now has two freeware children
>(Chime and Weblab) which incorporate key parts of Roger's brilliant source
>code.

 Make that three. I've got a Java applet at
http://www.rahul.net/pcm/dismol/DisMol.html
that originally started out as an enhancement to Will Ware's NanoCAD
applet, but I keep finding reasons to port more RasMol code to Java
to enable it to handle large molecules adequately.
 Currently it's only advantage over RasMol/Chime is that you can use it
to show others your molecules without requiring they install anything more
than a standard browser.
 I don't have any clear plans for further changes to this code, but I hope
to experiment with it as a UI for something like MMTK
(http://starship.skyport.net/crew/hinsen/mmtk.html) or Tinker.
-- 
------------------------------------------------------------------------
Peter McCluskey          | Critmail (http://crit.org/critmail.html):
http://www.rahul.net/pcm | Accept nothing less to archive your mailing list

++++------+------+------+------+------+------+------+------+------+------+
From: Toni Kazic <toni@athe.wustl.edu>
Subject: Re: Future of RasMol
Date: Mon, 6 Apr 1998 18:16:47 -0500 (CDT)
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: rasmol@dhcp-srv2.oit.umass.edu

Dear all,

I hope Roger reads this list (or Eric can provide a forwarding email) long
enough to receive his richly deserved praise and thanks.  To that I add my
voice -----

T H A N K S  R O G E R  AND  G  O  O  D      L  U  C  K!!!!!!!!!!!!

Toni

Toni Kazic, Ph.D.
Institute for Biomedical Computing
Box 8036
Washington University
700 South Euclid Ave.
St. Louis MO  63110

314-362-3121  (vox)
314-362-0234  (fax)

toni@athe.wustl.edu
http://ibc.wustl.edu/~toni

References: <0EQY00H1JGRCDW@rfd1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: Future of RasMol
Date: Mon, 06 Apr 1998 22:12:55 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

One question: Can we expect a improved version of Rasmol with
POVRay-output in the future (as it has been announced aproximately half
a year ago)???

Anyone still working on an improved Rasmol-version??

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

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++++------+------+------+------+------+------+------+------+------+------+
From: Roger Sayle <roger@metaphorics.com>
Subject: Re: Future of RasMol
Date: Tue, 7 Apr 1998 17:34:34 -0600 (MDT)
To: rasmol@dhcp-srv2.oit.umass.edu

On Mon, 6 Apr 1998, Marc Saric wrote:
> One question: Can we expect a improved version of Rasmol with
> POVRay-output in the future (as it has been announced aproximately half
> a year ago)???
> 
> Anyone still working on an improved Rasmol-version??

Arne Mueller with the Institut fuer Molekulare Genetik at the Univerity of
Goettingen <amuelle@gwdg.de> will shortly be making his patches to RasMol
available as version 2.6x1, which includes improved support for POV-ray
output.

Roger
--
Roger Sayle,                         E-mail: roger@metaphorics.com
Bioinformatics Group, Metaphorics,   WWW:    http://www.metaphorics.com/
419 East Palace Avenue,              Tel:    (+1) 505-984-0613
Santa Fe, New Mexico, 87501.         Fax:    (+1) 505-989-1200

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Noncovalent Bond Finder w/ Chime 2
Date: Wed, 08 Apr 1998 12:36:29 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Chimeleons:

I have developed an experimental Chime interface for quickly finding
noncovalent bonds, namely atom pairs between chains, or chains and ligands,
at suitable distances for hydrogen bonding or hydrophobic bonding.  It is
really easy to use (I hope!): you just load a PDB file from your computer
(automatic browse interface and load button), or one of the samples
provided, select a chain, ligand, or other moiety (any desired set of
atoms), and push a button.  The closest atoms to your target set are
highlighted.  Repeated button pushes move the finding shell out in 0.1
Angstrom increments. There is a tutorial demonstration on how to use it,
and lots of help, including a very basic intro to hydrogen bonds complete
with GIFs.

The Noncovalent Bond Finder REQUIRES Chime 2 (beta 2 is fine) and Navigator
4 (4.04 recommended). As has been discussed here previously, Chime 2 beta
is not yet available for the Macintosh (MDL is working hard on this as we
speak ...), and will NOT be developed for Win 3.1.  Therefore, you can only
do this on Win95 at the moment.

Try it at <http://www.umass.edu/microbio/chime/find-ncb/index.htm>

As always, you can download it for local use. (It took me 2 days of intense
effort from start to 'finish', tho I doubt that it's 'finished'. My wife
commented that I looked like a statue. :-)

Let me know what you think.  Please point out any misleading statements or
errors (I am not a hard-core chemist!).

Have fun, -Eric 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
RasMol Home Page (http://www.umass.edu/microbio/rasmol)
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <Pine.SOL.3.96.980407172926.17046B-100000@daylight>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: Future of RasMol
Date: Wed, 08 Apr 1998 19:46:48 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Roger Sayle wrote:

> Arne Mueller with the Institut fuer Molekulare Genetik at the
> Univerity of Goettingen <amuelle@gwdg.de> will shortly be making his 
> patches to RasMol available as version 2.6x1, which includes improved 
> support for POV-ray output.
Thanks for the info!

And thanks again for the great program -and good luck for the future!

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

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++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Noncovalent Bond Finder Upgraded
Date: Sun, 12 Apr 1998 23:22:00 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

My noncovalent bond finder has been further enhanced (now version 1.2).  In
particular, it should no longer crash Navigator constantly.  Also some
handy new capabilities were added.  More enhancements are planned. If you
have suggestions, please let me know.

http://www.umass.edu/microbio/chime/find-ncb/index.htm

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Most popular uses of the RasMol Home Page.
Date: Sun, 12 Apr 1998 23:33:35 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

This week (ending 4/11/98), I determined the numbers of accesses to
individual pages at the RasMol Home Page web site. There were a total of
4,024 visitors (unique IP addresses) during the 7-day period, consistent
with the past 5 weeks. These visitors fetched 78,792 files during the 7-day
period. Most of our visitors are interested in getting RasMol, and over
1,000/week download the program (consistent with last year's 41,000 total
downloads).  The second most popular use is finding PDB files (940 people),
and use of our new simplified PDB search interface is the 5th most popular
activity at the site (438 people). Third most popular is the RasMol Quick
Start document (888 people), and fourth, the gallery (500 people). 327
people consulted the RasMol reference manual.

While 265 people looked at the RasMol "movie" script page, only 67 scripts
were downloaded. If this keeps up, there will be over 3,000 "movie" script
downloads for the year, comparable to last year's 4,500 downloads.

Since I regard the "movie" script as an obsolete format, I was pleased that
there were 155 downloads of Chime packages, greater than the number of
downloads of RasMol "movie" scripts.  Last year there was only one Chime
package download for every 3 downloads of a "movie" script.  This week's
results predict 8,000 Chime package downloads for the year.

1,511 people visited the Chime site. A total of 606 of these people visited
the index pages of Chime presentations, pages which don't have a Chime
graphic plug-in.  Generally, less than 10% of these fetched files
consistent with actually having Chime installed.  So it appears that Chime
presentations at our site are being viewed by only about 50 people/week.
This might be an underestimate since there were 155 package downloads.  But
it suggests that nearly everyone who installs Chime and views these
presentations proceeds to download some of them, which I find surprising.

(Detailed data available on request.)
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Preston Garrison <GARRISONP@uthscsa.edu>
Subject: Stereo vectps
Date: Mon, 13 Apr 1998 19:01:52 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Hello all,

 Going through recent messages to the group, I noticed a question on doing
stereo vectps output from Rasmol. I recently figured out how to make this work.
In case anyone is interested, here is a brief description of what I did.
  First, get your molecule in the form, orientation and scale that you want. I
use the stereo mode to find the best view for my purpose, and write a script so
I can regenerate it easily. Then, turn stereo off and adjust the view
window to
give the aspect ratio that you need for the stereo image, generally wide in x
and short in y. Put the molecule in the center of the window and then do
translate -x to find an x value that puts it in the right place for the left
image. (If you want to print with the image separation used for publication,
your images should be about 6 cm apart center to center.) When you have it,
do a
write vectps filename. Now, do translate x to move to the right side the same
amount, do rotate y -6 (if you want the standard walleyed stereo; 6 if you
want
crosseyed stereo) and then do write vectps filename again. Now, you have to
edit
the EPS files in a text editor to get the images together. The vector
instructions begin about 80 lines into the file after 2 lines like this:

newpath 0 0 moveto 0 296 rlineto 716 0 rlineto 0 -296 rlineto
closepath clip 1 1 1 setrgbcolor fill

All you have to do is move the vector instructions for the right image into
the
left image file, appending them after the left image vector instructions and
before lines like these:

newpath 0 0 moveto 0 296 rlineto 716 0 rlineto 0 -296 rlineto
closepath 0 setgray 1 setlinewidth stroke
end grestore
showpage
%%Trailer
%%EOF

(The first 2 of these lines draw a box around the figure and can be deleted if
you don't want the box.) If you have text labels, the instructions for them
come
between the vector instructions and the lines above and look like this:

/Times-Roman findfont 16 scalefont setfont
0 0 0 setrgbcolor
(N) 420 179 Label
(C) 470 111 Label
(N) 674 148 Label
(C) 631 244 Label

 All the text instructions for both images should be moved to be together after
the vector instructions. The file can then be sent to a laser printer with a
printer utility (Apple Printer Utility on the Mac).
 I am ignorant of Postscript beyond what I figured out to do this, so warnings
of possible problems from the Postscript literate would be welcome.

Preston G.

Preston N. Garrison, Ph.D.
UTHSCSA-Biochem. Dept.
7703 Floyd Curl Dr.
San Antonio, TX 78284-7760
210-567-3702
garrisonp@arwen.uthscsa.edu

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Noncovalent Bond Finder Upgraded (again)
Date: Wed, 15 Apr 1998 10:30:27 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

My noncovalent bond finder has been further enhanced (now version 1.3). One
can now add to or replace the target (with atoms or residues) by clicking
on atoms with the mouse. Many additional minor improvements were made. 

http://www.umass.edu/microbio/chime/find-ncb/index.htm

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Scot Wherland <scot_wherland@wsu.edu>
Subject: Re: Noncovalent Bond Finder Upgraded (again)
Date: Fri, 17 Apr 1998 17:04:45 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

Eric,
I have been having some trouble with your ncb demo as follows.

I get the following errors going through the demo.
1. When the first view appears.
JavaScript Error: http://www.umass.edu/microbio/chime/find-ncb/gb.js, line
185:

top.fr_control.fr_control2.document.c2w_form has no properties.

2. After pressing "find" once
JavaScript Error: http://www.umass.edu/microbio/chime/find-ncb/msgcall.js,
line 136:

top.fr_control.fr_control2.document.c2w_form has no properties.

Likewise after pressing "find" again.

3. After clicking on the water molecule that appears.
JavaScript Error: http://www.umass.edu/microbio/chime/find-ncb/msgcall.js,
line 99:

top.fr_control.fr_control2.document.c2w_form has no properties.

Also, the name of the molecule appears (very briefly) in the same box that
gives the message "Document Done".

Eventually I get the "Too many java Script Errors".

I am running Communicator 4.01 and Chime 2.0.

I hope this is of some use to you.

Scot

At 10:30 AM 4/15/98 -0400, you wrote:
>My noncovalent bond finder has been further enhanced (now version 1.3). One
>can now add to or replace the target (with atoms or residues) by clicking
>on atoms with the mouse. Many additional minor improvements were made. 
>
>
>http://www.umass.edu/microbio/chime/find-ncb/index.htm
>
>/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
>Eric Martz, Professor (Immunology), Dept Microbiology
>Morrill IVN 203, U Mass, Amherst MA US 01003-5720
>413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
>UMass Chime Site <www.umass.edu/microbio/chime>
>- - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
Scot Wherland		       Voice: 509-335-3360
Prof. of Chemistry		FAX: 509-335-8867
Dept. of Chemistry		Email: scot_wherland@wsu.edu
Washington State University
Pullman, WA 99164-4630 USA

        edmolvis@dhcp-srv2.oit.umass.edu
References: <l03102804b15c1246ec9d@[128.151.30.51]>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Keeping centered while zooming
Date: Mon, 20 Apr 1998 12:17:22 -0400
To: mp19@ukc.ac.uk
Cc: dwrt@BPHVAX.biophysics.rochester.edu, rasmol@dhcp-srv2.oit.umass.edu,

Mayur Panchal poses the question: how can I keep an arbitrary atom or group
of atoms centered in the screen during zooming?

There is no good solution in RasMol.  Tim Maffett was kind enough to
implement my suggestion to cure this in Chime 1: the center of rotation
remains in the center of the screen during zooming by default.  You can
change the center to any prevously selected group of atoms with 'center
selected', or by clicking with the mouse following 'set picking center'.
Then zoom, and the new center snaps to the center of the screen and remains
there. This new default can be turned off with 'set zoom center off'.

RasMol fails to save the center of rotation in scripts ('save script
<filename>'), but Chime 2 saves it. You can add it by hand to the end of a
RasMol script using a select command followed with 'center selected'.

At very large zooms, the (invisible) edges of the molecule hit the
(invisible) space available to Chime, pushing the center off-center. The
only solutions I know to this are to reduce the zoom, or to save a smaller
subset of the atoms into a separate PDB file and use that.

For smooth zooms (and rotations) at speed independent of the computer's
speed, use Chime's 'move' command, which is documented at
http://www.umass.edu/microbio/chime/manual/chimeman.htm (but not yet at
MDL's site, tho other things are well documented there).

-Eric

At 4/16/98 , mp19 wrote:
>dear sir,
>I have been given your email in the hope that u 
>may be able to help me with a problem i am 
>facing with a chime-rasmol command.  please read the 
>following emails below : (originalyy to S. Dewhurst) 
>sincerely,
>mayur panchal.
>------------------------------------
>
>> >hello,
>> >my name is mayur panchal and i am an undergrad at the university of kent,
>> >i am currently doing a term project that involves setting up a webpage on
>> >calmodulin and in doing so....i came across your webpage
>> >(http:///www.urmc.rochester.edu/smd/mbi/grad/prframe.html).
>> >i am particularly impressed with the command that allows one to zoom into
>> >the molecule, to a precise site. I have looked at the sorce of the script
>> >and realise that you have zoomed into 2 monomers (with the numbers 25 for
>> >monomer A and B???). I would be very grateful if you could suggest how one
>> >is able to zoom in onto a specific atom/ or area when a molecule such as
>> >calmodulin is not a dimer???? and also how you were able to specify the
>> >different ranges of 'zoom' (in the chimescipt)????
>> >i would greatly appreciate your advice
>> >sincerely
>> >mayur
>> 
>>-------------------------------------------------------- 
>> actually, I have found zooming to specific regions to be hard.  In this
>> case, I got lucky (if I remember correctly).  In other cases, you can
>> reposition the image (x/y/z) before zooming, and this may work.  I think
>> there must be a better way, however -- I would contact Eric Martz and ask
>> him (emartz@microbio.umass.edu).  I'd be curious to know myself!
>> 
>> Best
>> 
>> Steve
>> 
>> 
>> Steve Dewhurst
>> Associate Professor, Department of Microbiology & Immunology
>> University of Rochester Medical Center
>> 575 Elmwood Avenue, Room 5-8106, Box 672.  Rochester, NY 14642
>> Tel.:(716)275-3216; FAX:(716)473-2361 OR 473-9573
>> http://www.urmc.rochester.edu/smd/mbi/steved.html
>> 
>
>----------------------
>mayur panchal
>mp19@ukc.ac.uk
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Noncovalent Bond Finder Upgraded to V1.41
Date: Wed, 22 Apr 1998 21:42:28 -0400
To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu

My noncovalent bond finder has been further enhanced (now version 1.41).
The initial radius can now be set at any desired value, the menu of
previously loaded PDB files now survives between sessions, residues can be
hidden with a mouse click, there is a command-line slot in the finder, a
"Find only" slot has been provided, some bugs were fixed, and other
improvements made.

Like all packages at my Chime site, this one has been downloadable as a
zipped file from version 1.0.  However I omitted to provide a link to the
download folder; an explicit link has now been provided (on the very first
page) for convenient downloading.

http://www.umass.edu/microbio/chime/find-ncb/index.htm

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

        rashie@bio.umass.edu, tdriscoll@amherst.edu
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Select Commands for Chime & RasMol
Date: Mon, 27 Apr 1998 20:05:27 -0400
To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu,

I finally got around to something I've wanted to do for a long time.  I've
written an overview of the expressions which can be used in commands to
select or restrict (hide) atoms, residues,  chains, ligands, groups of
residues using predefined terms, (such as hydrophobic or charged), defining
your own terms, and selecting nearest neighbors.

I even delved into RasMol's source code and found the amino acids
designated by the long mysterious predefined terms Surface, Buried, Small,
Medium, and Large.  (These definitions have now been added to the Reference
Manual as well.)

Look for "Select Commands in Chime and Rasmol" at

http://www.umass.edu/microbio/rasmol/seleccmd.htm

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Doug Brecknell <brecknel@chemistry.uq.edu.au>
Subject: A couple of problems with Chime 2.0 beta 2?
Date: Wed, 29 Apr 1998 17:26:08 +1000
To: rasmol@dhcp-srv2.oit.umass.edu

I have just started setting up some interactive Chime-based pages to cover
some simple stereochemical topics for my beginning organic chemistry
classes.  

One example is a simple XYZ animation showing the conformations of ethane
and butane resulting from rotation about the central C-C bond through 360
degrees.  I found that is is possible to select individual frames by frame
number using the "anim frame" command in the format "anim frame <frame
number>".  However, it seems that Chime 1.0 and 2.0 (beta 2) behave
differently here.  (In each case, I am using Chime with Netscape 4.05 on
Win 95)

To select 7th frame, the required value for <frame number> is 6 in both
Chime versions.  This suggests that the initial frame is frame # 0, and
this turns out to be the case for Chime 1.0.  However, in Chime 2.0 beta 2,
both "anim frame 0" and "anim frame 1" give the second frame, while "anim
frame 6" still gives the 7th frame, as in Chime 1.0.  In Chime 2.0, I have
found that I can reset the display to the initial frame using "anim frame
0; anim frame -1".  Fortunately, this does not seem to cause any problems
for Chime 1.0.  [With this work-around, I have been able to allow students
to select individual conformations (eclipsed, gauche etc) by clicking on
various buttons. See
http://www.chemistry.uq.edu.au/subjects/ch104/stereochem/vmkframe.html]

In another case, I was planning to use a script to load a series of
structures (without the limitations imposed by XYZ animations). I have not
found a successful way to use the "load" command in Chime 2.0 with MDL mol
files (even though this works OK in Chime 1.0)- I just get a black
background. In Chime 2.0, "load" works fine with both XYZ files and pdb
files (with or without the specific inclusion of the file format in both
cases).  The curious thing is that after "load mdl struc2.mol", the menu
command "File|Save Molecule As" saves the coordinates for the NEW structure
(struc2.mol) (even though the Chime window shows just a black background).

Any comments on either of these?

Doug Brecknell

*****************************************************************
Dr D.J. Brecknell                        Phone 61 7 3365 4019
Department of Chemistry                  Fax:  61 7 3365 4299
The University of Queensland
St Lucia
AUSTRALIA 4072          E-mail: brecknel@chemistry.uq.edu.au
*****************************************************************

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: A couple of problems with Chime 2.0 beta 2?
Date: Wed, 29 Apr 1998 10:09:43 -0400
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: bryan@mdli.com

Dear Doug:

Thanks for the detailed bug reports.  Bryan van Vliet, head of development
for Chemscape Chime at MDL, monitors this list so he can address the XYZ
frame numbering bug. They are working hard on Chime 2 and expect to have a
release out soon.  This is a good time to report bugs. I have given them a
list of about a dozen "killer" bugs which I hope they will be able to fix
for version 2, but I hadn't explored animation so I missed this one.

The inability to load mol files I also reported for Chime 2 beta 2.  I am
happy to report that this is fixed in the current version at MDL (they
provided me privately with beta 3).

-Eric

At 4/29/98 , you wrote:
>I have just started setting up some interactive Chime-based pages to cover
>some simple stereochemical topics for my beginning organic chemistry
>classes.  
>
>One example is a simple XYZ animation showing the conformations of ethane
>and butane resulting from rotation about the central C-C bond through 360
>degrees.  I found that is is possible to select individual frames by frame
>number using the "anim frame" command in the format "anim frame <frame
>number>".  However, it seems that Chime 1.0 and 2.0 (beta 2) behave
>differently here.  (In each case, I am using Chime with Netscape 4.05 on
>Win 95)
>
>To select 7th frame, the required value for <frame number> is 6 in both
>Chime versions.  This suggests that the initial frame is frame # 0, and
>this turns out to be the case for Chime 1.0.  However, in Chime 2.0 beta 2,
>both "anim frame 0" and "anim frame 1" give the second frame, while "anim
>frame 6" still gives the 7th frame, as in Chime 1.0.  In Chime 2.0, I have
>found that I can reset the display to the initial frame using "anim frame
>0; anim frame -1".  Fortunately, this does not seem to cause any problems
>for Chime 1.0.  [With this work-around, I have been able to allow students
>to select individual conformations (eclipsed, gauche etc) by clicking on
>various buttons. See
>http://www.chemistry.uq.edu.au/subjects/ch104/stereochem/vmkframe.html]
>
>In another case, I was planning to use a script to load a series of
>structures (without the limitations imposed by XYZ animations). I have not
>found a successful way to use the "load" command in Chime 2.0 with MDL mol
>files (even though this works OK in Chime 1.0)- I just get a black
>background. In Chime 2.0, "load" works fine with both XYZ files and pdb
>files (with or without the specific inclusion of the file format in both
>cases).  The curious thing is that after "load mdl struc2.mol", the menu
>command "File|Save Molecule As" saves the coordinates for the NEW structure
>(struc2.mol) (even though the Chime window shows just a black background).
>
>Any comments on either of these?
>
>Doug Brecknell
>
>
>*****************************************************************
>Dr D.J. Brecknell                        Phone 61 7 3365 4019
>Department of Chemistry                  Fax:  61 7 3365 4299
>The University of Queensland
>St Lucia
>AUSTRALIA 4072          E-mail: brecknel@chemistry.uq.edu.au
>*****************************************************************
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: "Kinemages" in Chime?
Date: Wed, 29 Apr 1998 10:40:05 -0400
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: dcr@suna.biochem.duke.edu

Speaking of animation, has anyone seen or succeeded in implementing a
kinemage-style overlay of alternative configurations of a molecule in
Chime?  (For example, oxy vs. deoxy hemoglobin.) I'm thinking this may be
possible using the NMR multi-model capability in Chime.  I'm planning to
try this soon, but would be glad to benefit from someone's experience.

I suspect it will be desirable to get the atomic coordinates of the two
configurations aligned, and I'm envisioning using Swiss-PDBViewer to save
aligned coordinates (http://www.umass.edu/microbio/rasmol/pdbtools.htm).

It is interesting how closely the user interface of David Richardson's
Kinemages presaged the type of web interface now customarily used in Chime.
 There was discussion last August between Tim Maffett (who was the
principal developer of Chime before his most unfortunate snowboarding
accident last December) and David Richardson about developing an automatic
kinemage -> Chime conversion program.  Sounds feasable and it would make
the 1,000+ extant kinemages web-deliverable, but it seems unlikely that
this will happen anytime soon, if ever (unless a volunteer steps forth).

-Eric
- - - 
Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US 01003-5720

RasMol Email List <www.umass.edu/microbio/rasmol/raslist.htm>

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: mmol and quaternary structure files
Date: Wed, 29 Apr 1998 10:47:01 -0400
To: Steve Dewhurst <dwrt@BPHVAX.biophysics.rochester.edu>
Cc: oeder@bnl.gov, rasmol@dhcp-srv2.oit.umass.edu

Dear Steve:

I am copying your message and my reply (below) to the email list in case
someone there can help.

At 4/29/98 , you wrote:
>Dear Eric
>
>I've been trying to look at some EBI files (obtained via the PDB; listed
>under quaternary structure files) of whole virions (ie, higher order
>assemblies of individual PDB subunits).  EBI refers to these as ".mmol"
>files and also claims to have Rasmol views ".pl".
>
>My problem is that I cannot seem to figure out how to view these files.
>I've downloaded as text, and then tried to open with RasMac.  My computer
>crashes.  The files are very big (eg, 1SVA is 70mB in .mmol format and
>about half that in the ".pl" format), and I'm not sure if this is a problem
>for Chime or for Rasmol...
>
>Any insight or advice would be much appreciated!
>
>Thanks
>
>Steve Dewhurst
>
>----------------------------------------------------------------
>Steve Dewhurst
>Associate Professor, Department of Microbiology & Immunology
>University of Rochester Medical Center
>575 Elmwood Avenue, Room 5-8106, Box 672.  Rochester, NY 14642
>Tel.:(716)275-3216; FAX:(716)473-2361 OR 473-9573
>http://www.urmc.rochester.edu/smd/mbi/steved.html
> 

The largest PDB file I ever tried in RasMol was a 48,000 alpha-carbon
rhinovirus capsid
(http://www.umass.edu/microbio/rasmol/whereget.htm#noncovalent).  RasMol
took minutes to generate each image (forget rotation!), but it didn't
crash.  Roger Sayle said, if I recall, that he had loaded up to half a
million atoms, but that may have been on unix.  So basically, I have no
help to offer, but I'll be interested if others have succeeded with this.

I don't know what mmol is.  ".pl" customarily stands for Perl source code.
I've copied this to Nancy Oeder at the PDB for any help she can offer. 
- - - 
Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US 01003-5720

RasMol Email List <www.umass.edu/microbio/rasmol/raslist.htm>

References: <0ES600A8XMB4F7@rfd1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: William R Mcclure <wm0p+@andrew.cmu.edu>
Subject: Re: "Kinemages" in Chime?
Date: Wed, 29 Apr 1998 14:28:27 -0400 (EDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Excerpts from mail: 29-Apr-98 "Kinemages" in Chime? by Eric
Martz@microbio.umas 
> Speaking of animation, has anyone seen or succeeded in implementing a
> kinemage-style overlay of alternative configurations of a molecule in
> Chime?

  The URL is to a course page where a series of Chime images shows the
course of an NMR refinement of a model peptide: 
http://info.bio.cmu.edu/courses/03438/NMRdemo/NMRdemo.html

  Chime 1.0 on a Mac doesn't permit independent selection, manipulation,
etc. using MODELn and ENDMDL statements in the PDB file, as can be done
in RasMol. Hence, the 3-5 models used in the above demo were all in one
PDB file. Not a problem for highlighting backbone conformations, but
probably less-than-terrific for showing small changes between large
structures.

-Will McClure 

++++------+------+------+------+------+------+------+------+------+------+
++++------+------+------+------+------+------+------+------+------+------+
From: Ozgur Huner <ohuner@oci.utoronto.ca>
Subject: Installing RasMol on Red Hat Linux 5.0
Date: Fri, 8 May 1998 17:17:56 -0400 (EDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Hi, all.  I couldn't find an answer to this problem in the RasMol EMail
history.  So, I thought that there may be someone out there who has
overcome this problem.

I'm installing RasMol 26b2 on Red Hat Linux 5.0.  After I do 'xmkmf' I see
the following error when I do 'make':

gcc -O2 -fno-strength-reduce     -I/usr/X11R6/include -I/include  -Dlinux
-D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_BSD_SOURCE
-D_SVID_SOURCE   -DFUNCPROTO=15 -DNARROWPROTO
-DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DEIGHTBIT   -c rasmol.c -o
rasmol.o
rasmol.c:46: sys/termio.h: No such file or directory
make: *** [rasmol.o] Error 1

The termio.h file cannot be found.  Where is this file from?

If anyone has successfully installed RasMol on RedHat 5.0 or can tell me
what the problem is, I would be very grateful.

Thanks,
Ozgur Huner
Ontario Cancer Institute

References: <Pine.SUN.3.91.980508171657.22296A-100000@gc>
++++------+------+------+------+------+------+------+------+------+------+
From: Christopher Hogue <hogue@mshri.on.ca>
Subject: Re: Installing RasMol on Red Hat Linux 5.0
Date: Fri, 08 May 1998 19:41:48 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Ozgur.

To find the file "termio.h" on your system.
Try:
cd /
find . -name "termio.h" -print

I have two Linux machines:
On RedHat 4.2 termio.h is in /usr/include/sys/termio.h
On RedHat 5.0 it is in /usr/include/termio.h

Try changing line 46 to remove the "sys/" in rasmol.c

---------------------------------------
Christopher W.V. Hogue, Ph.D.
Samuel Lunenfeld Research Institute
Mt. Sinai Hospital 600 University Ave.
Toronto Ontario Canada M5G 1X5
(416) 586-4800 xt2866
fax (416) 586-8857

hogue@mshri.on.ca

http://bioinfo.mshri.on.ca

Ozgur Huner wrote:
> 
> Hi, all.  I couldn't find an answer to this problem in the RasMol EMail
> history.  So, I thought that there may be someone out there who has
> overcome this problem.
> 
> I'm installing RasMol 26b2 on Red Hat Linux 5.0.  After I do 'xmkmf' I see
> the following error when I do 'make':
> 
> gcc -O2 -fno-strength-reduce     -I/usr/X11R6/include -I/include  -Dlinux
> -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_BSD_SOURCE
> -D_SVID_SOURCE   -DFUNCPROTO=15 -DNARROWPROTO
> -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DEIGHTBIT   -c rasmol.c -o
> rasmol.o
> rasmol.c:46: sys/termio.h: No such file or directory
> make: *** [rasmol.o] Error 1
> 
> The termio.h file cannot be found.  Where is this file from?
> 
> If anyone has successfully installed RasMol on RedHat 5.0 or can tell me
> what the problem is, I would be very grateful.
> 
> Thanks,
> Ozgur Huner
> Ontario Cancer Institute

X-Authentication-Warning: tom.fos.su.se: Host 416@klasa.fos.su.se [130.237.185.82] claimed to be struc.su.se
++++------+------+------+------+------+------+------+------+------+------+
From: "Klas M. Andersson" <klasa@struc.su.se>
Subject: Rasmol and Linux with X-Metro
Date: Fri, 15 May 1998 07:06:16 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

This is a multi-part message in MIME format.
--------------8056427C3D60944B59B6EEAC

Hi all,

I have tried to run the Linux-binary of Rasmol26b on my Linux machine
running RedHat 5.0 and X-Metro-server, but it does not work. It seems
that this is due to the X-Metro server rather than Linux OS since I have
been running the same binaries on Linux with XFree86.
However, the reason why I changed from XFree86 to X-Metro (commersial)
server was because the XFree86 graphic driver was (still is) not able
make use of more than 256 colours, so now I do not get any 'destroyed
colours' when using e.g. xv, xpaint (and hopefully Rasmol) etc.
I have also tried to compile Rasmol, but it does not work.
Has anybody out there any experience of Rasmol together X-Metro server?

Thanks!

Klas

--------------8056427C3D60944B59B6EEAC
Content-Description: Card for Klas  Andersson
Content-Disposition: attachment; filename="vcard.vcf"

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fn:             Klas  Andersson
n:              Andersson;Klas 
org:            Structural Chemistry
adr:            Arrhenius Laboratory;;Stockholm University;;;S-106 91  Stockholm;Sweden
email;internet: klasa@struc.su.se
title:          Ph. Lic./Crystallography
tel;work:       +46-8-16 25 70
tel;fax:        +46-8-16 31 18
tel;home:       -
note:           http://www.fos.su.se/~klasa/
x-mozilla-cpt:  ;0
x-mozilla-html: FALSE
version:        2.1
end:            vcard

--------------8056427C3D60944B59B6EEAC--

References: <355BE968.797743BC@struc.su.se>
++++------+------+------+------+------+------+------+------+------+------+
From: Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw>
Subject: Re: Rasmol and Linux with X-Metro
Date: Fri, 15 May 1998 17:44:15 +0800
To: rasmol@dhcp-srv2.oit.umass.edu

On Fri, May 15, 1998 at 07:06:16AM +0000, Klas M. Andersson wrote:
[cut]
> However, the reason why I changed from XFree86 to X-Metro (commersial)
> server was because the XFree86 graphic driver was (still is) not able
> make use of more than 256 colours, so now I do not get any 'destroyed
[cut]

    Well, you need to recompile rasmol for 16bit(or color
    depth other than 8bit) support.

-- 
Chen Hsiung Chan [¸âÂíºµ](BIG5)
Department of Life Science      http://waru.life.nthu.edu.tw/~frankch/
National Tsing Hua University   email: frankch@waru.life.nthu.edu.tw
Taiwan

References: <355BE968.797743BC@struc.su.se> <19980515174415.21630@waru.life.nthu.edu.tw>
X-Authentication-Warning: tom.fos.su.se: Host 416@klasa.fos.su.se [130.237.185.82] claimed to be struc.su.se
++++------+------+------+------+------+------+------+------+------+------+
From: "Klas M. Andersson" <klasa@struc.su.se>
Subject: Re: Rasmol and Linux with X-Metro
Date: Fri, 15 May 1998 11:29:11 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

This is a multi-part message in MIME format.
--------------BFA485D3E2F74FF5C18293D4

Chen Hsiung Chan wrote:

> On Fri, May 15, 1998 at 07:06:16AM +0000, Klas M. Andersson wrote:
> [cut]
> > However, the reason why I changed from XFree86 to X-Metro (commersial=
)
> > server was because the XFree86 graphic driver was (still is) not able=

> > make use of more than 256 colours, so now I do not get any 'destroyed=

> [cut]
>
>     Well, you need to recompile rasmol for 16bit(or color
>     depth other than 8bit) support.
>
> --
> Chen Hsiung Chan [=B8=E2=C2=ED=BA=B5](BIG5)
> Department of Life Science      http://waru.life.nthu.edu.tw/~frankch/
> National Tsing Hua University   email: frankch@waru.life.nthu.edu.tw
> Taiwan

Hi Chen,

Thanks for your reply. Unfortunately I do not think that is the problem.
Rasmol make use of the XFree86 library and this is not found since I use
X-Metro. When I try to compile using 32-bit, 16-bit or 8-bit I get the
following:

gcc -O2 -fno-strength-reduce     -I/usr/X11R6/include -I/include  -Dlinux=

-D__i3
86__ -D_POSIX_C_SOURCE=3D199309L -D_POSIX_SOURCE -D_BSD_SOURCE
-D_SVID_SOURCE   -D
FUNCPROTO=3D15 -DNARROWPROTO  -DRASMOLDIR=3D\"/usr/X11R6/lib/rasmol/\"
-DTHIRTYTWOBI
T   -c rasmol.c -o rasmol.o
rasmol.c: In function `OpenConnection':
rasmol.c:377: invalid use of undefined type `struct fd_set'
rasmol.c: In function `CloseConnection':
rasmol.c:394: invalid use of undefined type `struct fd_set'
rasmol.c: In function `InitTerminal':
rasmol.c:489: invalid use of undefined type `struct fd_set'
rasmol.c:489: invalid use of undefined type `struct fd_set'
rasmol.c:490: invalid use of undefined type `struct fd_set'
rasmol.c:496: invalid use of undefined type `struct fd_set'
rasmol.c:506: invalid use of undefined type `struct fd_set'
rasmol.c: In function `FetchCharacter':
rasmol.c:592: `WaitSet' has an incomplete type
rasmol.c:598: warning: passing arg 2 of `select' from incompatible pointe=
r
type
rasmol.c:598: warning: passing arg 3 of `select' from incompatible pointe=
r
type
rasmol.c:598: warning: passing arg 4 of `select' from incompatible pointe=
r
type
rasmol.c:603: invalid use of undefined type `struct fd_set'
rasmol.c:607: invalid use of undefined type `struct fd_set'
rasmol.c:611: invalid use of undefined type `struct fd_set'
rasmol.c: In function `main':
rasmol.c:1390: invalid use of undefined type `struct fd_set'
rasmol.c: At top level:
rasmol.c:120: storage size of `OrigWaitSet' isn't known
rasmol.c:121: storage size of `WaitSet' isn't known
make: *** [rasmol.o] Error 1

I do not know how to circumvent this rather than installing the Xfree86
package, but I am sure what will happen with X-Metro then.

Yours

/Klas

--------------BFA485D3E2F74FF5C18293D4
Content-Description: Card for Klas  Andersson
Content-Disposition: attachment; filename="vcard.vcf"

begin:          vcard
fn:             Klas  Andersson
n:              Andersson;Klas 
org:            Structural Chemistry
adr:            Arrhenius Laboratory;;Stockholm University;;;S-106 91  Stockholm;Sweden
email;internet: klasa@struc.su.se
title:          Ph. Lic./Crystallography
tel;work:       +46-8-16 25 70
tel;fax:        +46-8-16 31 18
tel;home:       -
note:           http://www.fos.su.se/~klasa/
x-mozilla-cpt:  ;0
x-mozilla-html: FALSE
version:        2.1
end:            vcard

--------------BFA485D3E2F74FF5C18293D4--

References: <355BE968.797743BC@struc.su.se> <19980515174415.21630@waru.life.nthu.edu.tw>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: Rasmol and Linux with X-Metro
Date: Fri, 15 May 1998 13:41:48 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Chen Hsiung Chan wrote:
> 
> On Fri, May 15, 1998 at 07:06:16AM +0000, Klas M. Andersson wrote:
> [cut]
> > However, the reason why I changed from XFree86 to X-Metro (commersial)
> > server was because the XFree86 graphic driver was (still is) not able
> > make use of more than 256 colours, so now I do not get any 'destroyed
> [cut]
> 
>     Well, you need to recompile rasmol for 16bit(or color
>     depth other than 8bit) support.

Hi All,

compiling RasMol fuer your unix-system is always a good idead, so you
can choose
how many colors to use.

First edit the 'Makefile'. Here you find iinformation about c-compiler
and important files for compilation.

Change the follwonig lines from:

CC = cc
CFLAGS = -O

to:

#CC = cc
#CFLAGS = -O

and: 

#CFLAGS_gcc      = -O -fomit-frame-pointer -fstrength-reduce
-finline-functions

to:

CFLAGS      = -O -fomit-frame-pointer -fstrength-reduce
-finline-functions

On a modern Linux-system this shell work, otherwise try to add the
follwing statement to the 'CFLAGS' line:

-I/usr/X11R6/include

if linking fails:

change the follwing line from:

# -lXi required if using DIALBOX
EXTLIBS = -lm -lXi -lXext -lX11

to:

# -lXi required if using DIALBOX
EXTLIBS = -lm -L/usr/X11R6/lib -lXi -lXext -lX11

Now you've to change the file 'rasmol.h', look for the follwog lines in
the beginning of the file:

#if !defined(EIGHTBIT) && !defined(THIRTYTWOBIT) && !defined(SIXTEENBIT)
/* #define THIRTYTWOBIT */
/* #define SIXTEENBIT   */
/* #define EIGHTBIT     */
#endif

If your X-Server runs with b-bit change the 'EIGHTBIT ' line to

#define EIGHTBIT 

only removing the comment characters

Do the same exclusively for the 'SIXTEENBIT' definition if have a
sixteen bit server or with 'THIRTYTWOBIT' if youßve a 32 OR 24 bit
server (it works with 24 bit!).

That's it now RasMol has to compile, if not please let me know (send me
an email).

	Good luck,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und 
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen        
Germany
phone: +49-551-399654   | fax  : +49-551-393805   
email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

References: <355BE968.797743BC@struc.su.se> <19980515174415.21630@waru.life.nthu.edu.tw> <355C2707.E5DC0326@struc.su.se>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: Rasmol and Linux with X-Metro
Date: Fri, 15 May 1998 13:54:44 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Klas M. Andersson wrote:
> 
> Chen Hsiung Chan wrote:
> 
> > On Fri, May 15, 1998 at 07:06:16AM +0000, Klas M. Andersson wrote:
> > [cut]
> > > However, the reason why I changed from XFree86 to X-Metro (commersial)
> > > server was because the XFree86 graphic driver was (still is) not able
> > > make use of more than 256 colours, so now I do not get any 'destroyed
> > [cut]
> >
> >     Well, you need to recompile rasmol for 16bit(or color
> >     depth other than 8bit) support.
> >
> > --
> > Chen Hsiung Chan [¸âÂíºµ](BIG5)
> > Department of Life Science      http://waru.life.nthu.edu.tw/~frankch/
> > National Tsing Hua University   email: frankch@waru.life.nthu.edu.tw
> > Taiwan
> 
> Hi Chen,
> 
> Thanks for your reply. Unfortunately I do not think that is the problem.
> Rasmol make use of the XFree86 library and this is not found since I use
> X-Metro. When I try to compile using 32-bit, 16-bit or 8-bit I get the
> following:
> 
> gcc -O2 -fno-strength-reduce     -I/usr/X11R6/include -I/include  -Dlinux
> -D__i3
> 86__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_BSD_SOURCE
> -D_SVID_SOURCE   -D
> FUNCPROTO=15 -DNARROWPROTO  -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\"
> -DTHIRTYTWOBI
> T   -c rasmol.c -o rasmol.o
> rasmol.c: In function `OpenConnection':
> rasmol.c:377: invalid use of undefined type `struct fd_set'
> rasmol.c: In function `CloseConnection':
> rasmol.c:394: invalid use of undefined type `struct fd_set'
> rasmol.c: In function `InitTerminal':
> rasmol.c:489: invalid use of undefined type `struct fd_set'
> rasmol.c:489: invalid use of undefined type `struct fd_set'
> rasmol.c:490: invalid use of undefined type `struct fd_set'
> rasmol.c:496: invalid use of undefined type `struct fd_set'
> rasmol.c:506: invalid use of undefined type `struct fd_set'
> rasmol.c: In function `FetchCharacter':
> rasmol.c:592: `WaitSet' has an incomplete type
> rasmol.c:598: warning: passing arg 2 of `select' from incompatible pointer
> type
> rasmol.c:598: warning: passing arg 3 of `select' from incompatible pointer
> type
> rasmol.c:598: warning: passing arg 4 of `select' from incompatible pointer
> type
> rasmol.c:603: invalid use of undefined type `struct fd_set'
> rasmol.c:607: invalid use of undefined type `struct fd_set'
> rasmol.c:611: invalid use of undefined type `struct fd_set'
> rasmol.c: In function `main':
> rasmol.c:1390: invalid use of undefined type `struct fd_set'
> rasmol.c: At top level:
> rasmol.c:120: storage size of `OrigWaitSet' isn't known
> rasmol.c:121: storage size of `WaitSet' isn't known
> make: *** [rasmol.o] Error 1

Ahh, that's the problem! 

I think you've installed a new linux-kernel, too! I'm currently busy
building a RasM0l-version that includes some small enhancements and one
bugfix. It's exactly the problem above. The linuxßkernel developer
changed something which is normally a structue to a typedefed structure.

If you want to fix the problem now, you can do the following:

Go to file 'rasmol.h' and insert the following line before the 'Default
user options':

/* define ´USE_FD_SET_TYPE´ if you get compilations  */
/* errors in ´rasmol.c´ claiming about ´WaitSet´     */
/* and OrigWaitSet´ (happens on newer linux systems) */
#define USE_FD_SET_TYPE

Now open #rasmol.c' and look for the follwoing lines (lines 120,121):

static struct fd_set OrigWaitSet;
static struct fd_set WaitSet;

change it to:

#ifdef USE_FD_SET_TYPE /* e.g. linux 2.0.33 typedef´s this structure! */
#define fd_set fd_set
#else
#define fd_set struct fd_set
#endif           
static fd_set OrigWaitSet;
static fd_set WaitSet;      

Then change all strings 'struct fd_set' to 'fd_set' (these are lines
597, 598).
Now RasMol has to compile.

> I do not know how to circumvent this rather than installing the Xfree86
> package, but I am sure what will happen with X-Metro then.
> 
> Yours
> 
> /Klas
> 

	best wishes,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und 
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen        
Germany
phone: +49-551-399654   | fax  : +49-551-393805   
email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

References: <355BE968.797743BC@struc.su.se> <19980515174415.21630@waru.life.nthu.edu.tw> <355C2707.E5DC0326@struc.su.se> <355C4924.C53A449@gwdg.de>
++++------+------+------+------+------+------+------+------+------+------+
From: Juan Casero <casero@beowulf.cox.miami.edu>
Subject: Re: Rasmol and Linux with X-Metro
Date: Sat, 16 May 1998 23:30:39 +0000
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: rasmol@dhcp-srv2.oit.umass.edu

Arne Mueller wrote:

> Klas M. Andersson wrote:
> >
> > Chen Hsiung Chan wrote:
> >
> > > On Fri, May 15, 1998 at 07:06:16AM +0000, Klas M. Andersson wrote:
> > > [cut]
> > > > However, the reason why I changed from XFree86 to X-Metro (commersial)
> > > > server was because the XFree86 graphic driver was (still is) not able
> > > > make use of more than 256 colours, so now I do not get any 'destroyed
> > > [cut]
> > >
> > >     Well, you need to recompile rasmol for 16bit(or color
> > >     depth other than 8bit) support.
> > >
> > > --
> > > Chen Hsiung Chan [¸âÂíºµ](BIG5)
> > > Department of Life Science      http://waru.life.nthu.edu.tw/~frankch/
> > > National Tsing Hua University   email: frankch@waru.life.nthu.edu.tw
> > > Taiwan
> >
> > Hi Chen,
> >
> > Thanks for your reply. Unfortunately I do not think that is the problem.
> > Rasmol make use of the XFree86 library and this is not found since I use
> > X-Metro. When I try to compile using 32-bit, 16-bit or 8-bit I get the
> > following:
> >
> > gcc -O2 -fno-strength-reduce     -I/usr/X11R6/include -I/include  -Dlinux
> > -D__i3
> > 86__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_BSD_SOURCE
> > -D_SVID_SOURCE   -D
> > FUNCPROTO=15 -DNARROWPROTO  -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\"
> > -DTHIRTYTWOBI
> > T   -c rasmol.c -o rasmol.o
> > rasmol.c: In function `OpenConnection':
> > rasmol.c:377: invalid use of undefined type `struct fd_set'
> > rasmol.c: In function `CloseConnection':
> > rasmol.c:394: invalid use of undefined type `struct fd_set'
> > rasmol.c: In function `InitTerminal':
> > rasmol.c:489: invalid use of undefined type `struct fd_set'
> > rasmol.c:489: invalid use of undefined type `struct fd_set'
> > rasmol.c:490: invalid use of undefined type `struct fd_set'
> > rasmol.c:496: invalid use of undefined type `struct fd_set'
> > rasmol.c:506: invalid use of undefined type `struct fd_set'
> > rasmol.c: In function `FetchCharacter':
> > rasmol.c:592: `WaitSet' has an incomplete type
> > rasmol.c:598: warning: passing arg 2 of `select' from incompatible pointer
> > type
> > rasmol.c:598: warning: passing arg 3 of `select' from incompatible pointer
> > type
> > rasmol.c:598: warning: passing arg 4 of `select' from incompatible pointer
> > type
> > rasmol.c:603: invalid use of undefined type `struct fd_set'
> > rasmol.c:607: invalid use of undefined type `struct fd_set'
> > rasmol.c:611: invalid use of undefined type `struct fd_set'
> > rasmol.c: In function `main':
> > rasmol.c:1390: invalid use of undefined type `struct fd_set'
> > rasmol.c: At top level:
> > rasmol.c:120: storage size of `OrigWaitSet' isn't known
> > rasmol.c:121: storage size of `WaitSet' isn't known
> > make: *** [rasmol.o] Error 1
>
> Ahh, that's the problem!
>
> I think you've installed a new linux-kernel, too! I'm currently busy
> building a RasM0l-version that includes some small enhancements and one
> bugfix. It's exactly the problem above. The linuxßkernel developer
> changed something which is normally a structue to a typedefed structure.
>
> If you want to fix the problem now, you can do the following:
>
> Go to file 'rasmol.h' and insert the following line before the 'Default
> user options':
>
> /* define ´USE_FD_SET_TYPE´ if you get compilations  */
> /* errors in ´rasmol.c´ claiming about ´WaitSet´     */
> /* and OrigWaitSet´ (happens on newer linux systems) */
> #define USE_FD_SET_TYPE
>
> Now open #rasmol.c' and look for the follwoing lines (lines 120,121):
>
> static struct fd_set OrigWaitSet;
> static struct fd_set WaitSet;
>
> change it to:
>
> #ifdef USE_FD_SET_TYPE /* e.g. linux 2.0.33 typedef´s this structure! */
> #define fd_set fd_set
> #else
> #define fd_set struct fd_set
> #endif
> static fd_set OrigWaitSet;
> static fd_set WaitSet;
>
> Then change all strings 'struct fd_set' to 'fd_set' (these are lines
> 597, 598).
> Now RasMol has to compile.
>
> > I do not know how to circumvent this rather than installing the Xfree86
> > package, but I am sure what will happen with X-Metro then.
> >
> > Yours
> >
> > /Klas
> >
>
>         best wishes,
>
>         Arne
>
> --
> Arne Mueller
> Institut fuer Mikrobiologie und Genetik
> Abt. Molekulare Genetik und
> Praeparative Molekularbiologie
> Universitaet Goettingen
> Grisebachstr. 8
> 37077 Goettingen
> Germany
> phone: +49-551-399654   | fax  : +49-551-393805
> email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

Arne -

Thanks alot for posting this.  About two months ago I was stuck trying to
compile RasMol26b2 because of the struct fd_set issue.  The information you
gave me above helped me to compile RasMol26b2 on a RedHat 5.0 Linux box with
XFree86 3.3.2 and 16 bit color mode.  This system is only a Am5x86 running at
133 Mhz with a VLB at 33 Mhz but even so RasMol is very fast and responsive on
it.

Thanks.......

--
Juan Casero
email:  casero@beowulf.cox.miami.edu
   __   _
  / /  (_)__  __ ____  __
 / /__/ / _ \/ // /\ \/ /  . . .  t h e   c h o i c e   o f   a
/____/_/_//_/\_,_/ /_/\_\              G N U   g e n e r a t i o n . . .

++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Announce: RasMol
Date: Sun, 17 May 1998 21:03:01 +0000
To: Rasmol Mailinglist <rasmol@dhcp-srv2.oit.umass.edu>
Cc: PDB Mailing List <pdb-l@pdb.pdb.bnl.gov>

Dear All,

Some weeks ago I´ve told some of you  I've prepared some small
patches to Roger Sayle's RasMol, this was in context of a 
discussion we had in the pdb mailinglist about cispeptides. 
I'm sorry that it took so long to announce my patches (including
one to identify cispeptides). Here they are ...

you can download the sources from:
 
	ftp://nexus.roko.goe.net/pub/rasmol/

here's the a copy of the README.ext file I've written to describe the 
patches, please note that's still a beta release and I cannot guarantee 
for the correctness of the program (I think nobody can do this ...). The
release of these patches is in agreement with Roger Sayle.

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

			    RasMol 2.6x1
              Molecular Graphics Visualisation tool.

                           Roger Sayle, 1995
			   Arne Mueller, 1998	

This is the description of some extensions to RasMol version 2.6beta
from 
October 1996 from Roger Sayle. 

Here´s the list of exstensions I´ve applied to RasMol:
======================================================

1. ability to list all chains, groups or atoms of current selection

	show selected <atom | group | chain>
	
2. list phipsi angles of current selection
	
	show phipsi

3. export phipsi angles as datafile for Ramachandran plots

	write ramachan

4. omega angle (cisbonded peptids) as regular expression

	set cisangle INTEGER_VALUE
	select cisbonded 
	select cisbonded and pro
        ...

5. export current representation as POVRay file

	write povray FILENAME

Description and usage of the new commands and expressions:
===========================================================

1. "show selected"
-----------------
   
This command is an extension of the existing "show" command.
It lists all currently selected groups of your molecule. You get the 
following information:
- chain identifier (if there is more then one chain!)
- group name
- residue number (of the group)		
- secondary structure state of the group, Helix (H), Sheet (S), Turn
(T),   
  Coil (C), this is  for aminoacids only
- the number of atoms of this group that are selected and the
  absolute number of atoms in the group		

example:
 
load the molecule "3crn.pdb" from the RasMol-data directory. This is the 
CRO-Repressor from lambda phage which binds to specific lambda-DNA as a 
dimer. Maybe you are interested in quikly listing all residues of the 
protein near by DNA and so possibly involved in DNA-binding. In a first 
step you can use the existing "select within" expression for this.  
    	
here´s a section of my RasMol-commandline:

	RasMol> color chain
	RasMol> select within(3.5, DNA) and Protein
	69 atoms selected!
	RasMol> color red 			
	RasMol> show selected
	Chain: L  Group:  ARG  10 (H)   (1/11)  atoms
	Chain: L  Group:  THR  16 (H)   (1/7)   atoms
	Chain: L  Group:  GLN  17 (H)   (4/9)   atoms
	Chain: L  Group:  LYS  27 (C)   (4/9)   atoms
	Chain: L  Group:  GLN  28 (H)   (2/9)   atoms
	Chain: L  Group:  GLN  29 (H)   (3/9)   atoms
	Chain: L  Group:  SER  30 (H)   (2/6)   atoms
	Chain: L  Group:  GLN  32 (H)   (3/9)   atoms
	Chain: L  Group:  LYS  40 (C)   (1/9)   atoms
	Chain: L  Group:  ARG  41 (C)   (2/11)  atoms
	Chain: L  Group:  PRO  42 (C)   (1/7)   atoms
	Chain: L  Group:  ARG  43 (C)   (5/11)  atoms
	Chain: L  Group:  PHE  44 (C)   (3/11)  atoms
	Chain: R  Group:  ARG  10 (H)   (1/11)  atoms
	Chain: R  Group:  THR  16 (H)   (2/7)   atoms
	Chain: R  Group:  GLN  17 (H)   (3/9)   atoms
	Chain: R  Group:  LYS  27 (C)   (2/9)   atoms
	Chain: R  Group:  GLN  28 (H)   (2/9)   atoms
	Chain: R  Group:  GLN  29 (H)   (3/9)   atoms
	Chain: R  Group:  SER  30 (H)   (1/6)   atoms
	Chain: R  Group:  GLN  32 (H)   (2/9)   atoms
	Chain: R  Group:  LEU  33 (H)   (1/8)   atoms
	Chain: R  Group:  LYS  40 (C)   (1/9)   atoms
	Chain: R  Group:  ARG  41 (C)   (5/11)  atoms
	Chain: R  Group:  ARG  43 (C)   (3/11)  atoms
	Chain: R  Group:  PHE  44 (C)   (3/11)  atoms     	
    
What happens?	
     
First I color the molecules by chain, so that every chain has it´s own 
color. Then I select all groups of the molecules that are within a
radius 
of 3.5 Angstom from the DNA (measured from any point inside the DNA 
molecule) and that are part of the protein. RasMol reports that 69 Atoms 
has been selected. Now we can visualize the atoms with the third command
that colors these atoms in red. The extension of the "show" command can
now be 
helpfull to list all the groups (aminoacids) that are selected with
additional
information on the command-window. Let me explain the last line of the
RasMol
output: It says that there´s selected a group of Chain ´R´, it´s
Phenylalanin 
residue 44 which is located in a Coil (or Turn), Phenylalanin consits of
11 
atoms but only 3 are in the current selection (means that there are only
3 of 
11 atoms inside a distance of 3.5 Angstrom of the DNA).

Extensions of the "show selected" command:
------------------------------------------
 
The following long forms of the commad are available:

	show selected atom
	show selected group  ( same as "show selected" )
	show selected chain	

Assume you´re only interested in the aromatic groups of the above
selection,
here´s my RasMol-commandline:
	
	RasMol> select selected and aromatic
	6 atoms selected!  
	RasMol> show selected atom
	Chain: L  Group:  PHE  44 (C)  Atom:  N   1182
	Chain: L  Group:  PHE  44 (C)  Atom:  CD2 1189
	Chain: L  Group:  PHE  44 (C)  Atom:  CE2 1191
	Chain: R  Group:  PHE  44 (C)  Atom:  N   1747
	Chain: R  Group:  PHE  44 (C)  Atom:  CD1 1753
	Chain: R  Group:  PHE  44 (C)  Atom:  CE1 1755  
	RasMol> show selected chain
	Chain: L        no group completely selected
	Chain: R        no group completely selected  

"select selected and aromatic" means that you coose te aromatic subset
of your current selection (a quick way). I list all the selected atoms,
and you see these atoms are in Phenylalanins of two chains (both with
residue number 44). The last two columns give you a detailed description
of the atom in your selection. At last, there´s no group completely
selected.
Even there are some selected atoms in each chain there must be at least
one 
group in a chain completely selected to produce informative output! 

look at this:

	RasMol> select aromatic
	96 atoms selected! 
	RasMol> show selected chain
	Chain: L        (4/66)  groups
	Chain: R        (4/64)  groups  

You select all aromatic aminoacids of all chains (these are 4 of a total
of
66 in chain L). 

2. PHI-PSI Angles
-----------------

In the current patchlevel you cannot youse phi/psi angle information as
a regular expression to select residues but you can list the phi/psi
angle 
combination of the currently selected residues.

... assume you continue from the recent selection above:

	RasMol> show phipsi
	Chain: L  Group:  PHE  44 (C)   Phi = -100.6    Psi = 25.68
	Chain: L  Group:  PHE  46 (H)   Phi = -103.3    Psi = -40.62
	Chain: L  Group:  TRP  58 (H)   Phi = -75.01    Psi = -44.79
	Chain: L  Group:  TYR  61 (H)   Phi = -119.2    Psi = 161.4
	Chain: R  Group:  PHE  44 (C)   Phi = -91.57    Psi = 7.374
	Chain: R  Group:  PHE  46 (H)   Phi = -77.93    Psi = -23.86
	Chain: R  Group:  TRP  58 (H)   Phi = -51.71    Psi = -43.06
	Chain: R  Group:  TYR  61 (H)   Phi = -121.5    Psi = -135.1    

The last line of the output tells you Thyrosin 61 in chain R is in a
Helix 
and has a phi/psi combination of -121.5/-135.1 degrees. The angles are 
measure in degrees from -180.0 to +180.0. 

3. Writing a datafile with PHI-PSI Angle information:
-----------------------------------------------------

You can write the phi/psi angle combinations of any kind of selection
into a datafile. Non-aminoacid groups are skipped.

To write the above angles into a file with name "aromatic.ang" do this:

	RasMol> write ramachan "aromatic.ang" 

The contens of the file is then:

# File: aromatic.ang
# Creator: RasMol Version 2.6
# from Molecule: 434 CRO PROTEIN COMPLEX WITH 20 BASE PAIR PIECE OF
/DNA$
# Brookhaven Code: 3CRO
# phi/psi-angles for Ramachandran-Plot
#
#               Phi      Psi
PHE     L44     -100.6  25.68
PHE     L46     -103.3  -40.62
TRP     L58     -75.01  -44.79
TYR     L61     -119.2  161.4
PHE     R44     -91.57  7.374
PHE     R46     -77.93  -23.86
TRP     R58     -51.71  -43.06
TYR     R61     -121.5  -135.1   

Column two summarizes the chain and residue number. Every kind of
plotting 
program shoud be able to plot an appropiate graph (Ramachandran Plot). I 
prefere gnuplot, you can get it for free from:
	
	ftp://ftp.gwdg.de/pub/gnu/gnuplot-3.5.tar.gz 
	for the much more powerfull version 3.6 beta look at
	ftp://cmpc1.phys.soton.ac.uk/pub/

Call gnuplot from the command-line and ...

	gnuplot> plot "aromatic.ang" using 3:4 

will procude a basic Ramachandran Plot (you´ve only to adjust scaling of
the 
axes).

To save data for a complte Ramachandran Plot you should select all
residues 
expect Glycin, because it has fuzzy phi/psi angle combinations:

	RasMol> select not gly
	1857 atoms selected!     
	
Off course this data representation is not the very best because you´d
like to
produce a contour plot or something three dimensional so you can
identify 
regions where datapoints are very crowded - maybe I´ll change this in
future.

4. Identifieing Cispeptides from Omega angles:
----------------------------------------------
 
A peptidebond connecting two aminoacids is in a mesomeric state - it's 
somewhere between singel- and double-bond. Normally the torsion angle
(this 
is omega) of souch a peptidebond is between 170 and 180 degrees, where
the 
carboxyl groups of the two aminoacids point in different directions so
that 
there is a maximum space between these groups, this geometry is locally
the 
most favorible. This omega angle state is the 'trans' state. If the
carboxyl 
goups are on the same site of the two residues they bump each other, in
this 
case the omega angle is geometrically in cis state and is  normally
smaller 
10 degrees. Normally all residues are in trans state, but there are
exeptions 
especially for Prolines. It can be very usefull to know about
cispeptides 
when studing a protein with RasMol. 

The protein Ribonuclease T1 (pdb code '1det') contains two prolines with
omega 
angles in cis. 

Here's a pice of my RasMol-commandline which identifies these groups:

	RasMol>  color white
	RasMol> select
	892 atoms selected!
	RasMol>  color white
	RasMol> set cisangle 10
	RasMol>  select cisbonded
	32 atoms selected!
	RasMol>  select cisbonded
	32 atoms selected!
	RasMol> color red
	RasMol>  show phipsi
          Group:  TYR  38 (C)   Phi = -94.72    Psi = 139.1
	  Group:  PRO  39 (C)   Phi = -79.79    Psi = 161.1     Omega = -0.1959
          Group:  SER  54 (C)   Phi = -89.17    Psi = 171.2
          Group:  PRO  55 (C)   Phi = -68.15    Psi = 153.2     Omega =
3.128

After coloring the whole molecule in white I set the cutoff for
identifing 
cis peptidbonds to 10 degrees. Then I select all peptides in cis state
and 
visualize these with red color in the RasMol display. I list the phi/psi
angle
combinations of the selected residues, in case that there are
cis-peptides. The
'show phipsi' command also lists the omega angles (but these are ignored
in 
the 'write ramachan' command!).  

You don't need to set the cutoff for the omega angle, the default value
is 90 
degrees.

4. Export the current graphical representation tp POVRay:
---------------------------------------------------------

POVRay is a raytracer. A raytracer can calculate a photorealistic image
with light models in  high quality graphics from a 3D-description which 
could be e.g a molecule.  

I extended the export function for RasMol that writes a POVRay input
file.

usage

	write povray FILENAME	

'FILENAME' must not' have the extension '.pov', because RasMol writes
two 
files:

	FILENAME.pov
	FILENAME.inc

The '.pov' file containts the global description of the scene (molecule)
with
parameters you can change. The '.inc' contains all data for the scene to 
render, don't touch it. 

Description of the '.pov' file:

The first part of the file contains information about the view and the
light 
source of the scene - you should be carefull to change it. 'View'
(camera), 
'light_source' and background (colour) is taken from the current RasMol 
representaion.

The 'Union' that follows contains general defenitions which are applied
on 
all elements of the molecule. These are:

	- specular 0.5
	- roughness 0.01
	- diffuse 0.8
	- ambient 0.2
	
If you don't like the default values for the elumination model you can
test 
different values for these parameters. The default values produce a
slightly 
diffuse light, the 'material' the elements of the molecule are made of
is a
bit shiny (smooth), it´s related to the 'specular' elumination in
RasMol.

	- #declare T = 0

You can set 'T' to a value between '1.0' (solid) and '0.0' (complete 
transparent). Setting it to '0.8' you´ve a slightly transparent
molecule. This
might be usefull for combining two representations:

Combining two ore more representations:

You can create more than one representation of your molecule with
RasMol. Save 
eaach representation with 'write povray represx' (where x is 1, 2, ...).
Edit 
then one '.pov' file, e.g. to combine 'repres1' with ´repres2´ edit
'repres1.pov':

	#declare T = 0
	#include "repres1.inc"
	
to:

	#declare T = 0
	#include "repres1.inc"
	#declare T = 0
	#include "repres2.inc"	

Then POVRay combines both representations. You can also make one of
these
a little transparent by changing the 'T´ parameter, uncomment the
'hollow'
parameter for this (as the name indicates it renders the model hollow).

Don't touch the transformations matrix! RasMol uses the original
coordinats 
of the pdb-file and applies a transformation matrix on it to realize
rotation,
zooming and translation.

For testing a POV-file you can uncomment '//no_shadow' to 'no_shadow',
POVRay
doesn't calculate any shadow then which is much quicker in rendering. 

RasMol features supportet from the POVRay export-filter:
-------------------------------------------------------

- geometric transformation (rotation, translation, zooming)
- spheres
- cylinders (including wireframe and backbone)
- dots
- SS- and H-Bonds
- colours

The concept is to create a high quality inmage with POVRay that's
identical
with the representation in RasMol (expect it's quality).

RasMol feature _NOT_ yet supportet from the POVRay export-filter:
-----------------------------------------------------------------

- curved representations (cartoons, trace, ribbons)
  This is because RasMol doesn't save any triangles which build the
curved
  elements (this is also the reason why RasMol cannot save these 
  representations as vector postscript at the moment). I hope to find a
way
  to export  these things to POVRay since cartoons are frequnetly
used.	  
	
- dotted lines
  just forgot this feature ;-) . I´ll fix it.

- slabbing
  Ugly problem. Because RasMol uses a transformation matrix the slab
plane
  is transformed, too, this results in a strange slabbing when rotating
or
  zooming the molecule. I´ve to apply a reverse transformation matrix to
  the slab plane (haven´t done this yet ...).
  
- labels
  In general no problem in POVRay version 3, but I havn't yet decided
  how to place labeles. There´s also the same matrix problem as with
slabbing.

- stereo
  not yet implemented

I hope to fix these things in future, but I don't know when there´ll be
a
"perfect" POVRay output.

POVRay:
-------

Use the command:

	write povray myfile

to write a POVRay-file,

you can render it on a unix-commandline with:

	povray +Imyfile.pov +Omyfile.tga +H400 +W400 +v  

You´ll get a 400x400 TGA-image with name 'myfile.tga'.

You can download POVRay for nearly all platforms, look at

	http://www.povray.org/

Some important notes:
---------------------

- on linux-systems with newer kermel-versions (e.g. 2.0.33) you
  get compilation errors in 'rasmol.c' with 'fd_set'. If so uncomment
  #define USE_FD_SET_TYPE in `rasmol.h`.

- There's a known bug in RasMol. It'll crash when first choosing a large
zoom 
  factor with wireframe or spacefill representation and then switching
to 
  backbone, cartoons, trace or ribbons! Maybe I can fix this in future.

- The file 'rasmol.hlp' hasn't been updated with my changes.

- Currently there are no executables of the patched RasMol version
available, 
  you´ve to compile the sourcecode yourself, but it shell work, since
there
  are no changes in platform specific parts (see file 'INSTALL' for
details). 
  I hope to build a Mac and a win95/NT executable as soon as possible. 
  
  >>> IF YOU BUILD AN EXECUTALBE FOR MAC OR WIN PLEASE LET ME KNOW <<<

Download the patch or the patched version:
------------------------------------------

You can get the patch and the complete version from

ftp://nexus.roko.goe.net/pub/rasmol/
( ftp://134.76.63.65/pub/rasmol )

Patching your old RasMol2.6b version from October 96 (for unix):
----------------------------------------------------------------

Copy the patch-file in the RasMol source directory and do the following:

patch -p1 <  patchfile 2>&1 | tee patched.prot 

A report of the patch will be created in 'patched.prot', look in it for
the 
string "failed", if you find it something went wrong and you've to get
the 
complete patched version, otherwise you can recompile your patched
Rasmol. 

  
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Please report bugs and suggestions to:

Arne Mueller
amuelle3@gwdg.de

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und 
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen        
Germany
phone: +49-551-399654   | fax  : +49-551-393805   
email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: cispeps - finding them without using dihedral angles
Date: Sun, 17 May 1998 15:12:57 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Hooray to Arne Mueller for his improved RasMol!
Please let us Windows95 users and Mac users know as soon as a binary is
available ready to run for those of us who don't want to learn how to compile
the source code.

As Byungkook (BK) Lee pointed out on the PDB email list (to subscribe or
review
the history, see
http://www.pdb.bnl.gov/pdb-docs/pdb-l.html - the paper is 
Fold Des 1998;3(1):1-10 
A new procedure for constructing peptides into a given Calpha chain.
Wang Y, Huq HI, de la Cruz XF, Lee B
Pubmed
<http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9502315&form=6&db=
m&Dopt=b>http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9502315&fo
rm=6&db=m&Dopt=b
but I haven't seen the part which discusses cispeps)
you can also find cis peptide bonds by c-alpha distance.  Below is a RasMol
script cispeps.spt which will do this, provided there are no residue numbers
greater than 999.  The script calls a subscript, odd.spt (also below) which
first selects every odd-numbered residue.  Then it uses the 'within'
command to
find even-numbered alpha carbons close enough to be cis peptide bonded.

The file 1cbx.pdb is a good example as it not only has one of the common Pro-X
cis peptide bonds, but also two of the rare cases of cis peptide bonds where
neither AA is Pro.

FILE cispeps.spt
-----------------------------------------------------------
# TURN OFF ALL REPRESENTATIONS
select all
script "repsoff.spt"
#show blank till finished
refresh

# SHOW CHAIN-COLORED BACKBONE TRACE
backbone 0
color chain

# FIND CIS PEPTIDE BONDED PAIRS OF AA's

script "odd.spt" # GOOD ONLY FOR RESIDUES 1-1000!!
select odd and *.ca
select within(3.3, selected) and *.ca and not selected

#find the other members of the pairs
select selected or (*.ca and within(3.3, selected))
spacefill 0.5
define cispeps selected
color magenta

#add the intervening backbone bonds
select selected or within(1.8, selected)
wireframe 0.2

select within(1.8, cispeps) and not cispeps
color cpk

select cispeps

--------------------------------------------------------------------
file odd.spt
--------------------------------------------------------------------
select 1,3,5,7,9
select selected or 11,13,15,17,19,21,23,25,27,29
select selected or 31,33,35,37,39,41,43,45,47,49
select selected or 51,53,55,57,59,61,63,65,67,69
select selected or 71,73,75,77,79,81,83,85,87,89
select selected or 91,93,95,97,99

select selected or 101,103,105,107,109
select selected or 111,113,115,117,119,121,123,125,127,129
select selected or 131,133,135,137,139,141,143,145,147,149
select selected or 151,153,155,157,159,161,163,165,167,169
select selected or 171,173,175,177,179,181,183,185,187,189
select selected or 191,193,195,197,199

select selected or 201,203,205,207,209
select selected or 211,213,215,217,219,221,223,225,227,229
select selected or 231,233,235,237,239,241,243,245,247,249
select selected or 251,253,255,257,259,261,263,265,267,269
select selected or 271,273,275,277,279,281,283,285,287,289
select selected or 291,293,295,297,299

select selected or 301,303,305,307,309
select selected or 311,313,315,317,319,321,323,325,327,329
select selected or 331,333,335,337,339,341,343,345,347,349
select selected or 351,353,355,357,359,361,363,365,367,369
select selected or 371,373,375,377,379,381,383,385,387,389
select selected or 391,393,395,397,399

select selected or 401,403,405,407,409
select selected or 411,413,415,417,419,421,423,425,427,429
select selected or 431,433,435,437,439,441,443,445,447,449
select selected or 451,453,455,457,459,461,463,465,467,469
select selected or 471,473,475,477,479,481,483,485,487,489
select selected or 491,493,495,497,499

select selected or 501,503,505,507,509
select selected or 511,513,515,517,519,521,523,525,527,529
select selected or 531,533,535,537,539,541,543,545,547,549
select selected or 551,553,555,557,559,561,563,565,567,569
select selected or 571,573,575,577,579,581,583,585,587,589
select selected or 591,593,595,597,599

select selected or 601,603,605,607,609
select selected or 611,613,615,617,619,621,623,625,627,629
select selected or 631,633,635,637,639,641,643,645,647,649
select selected or 651,653,655,657,659,661,663,665,667,669
select selected or 671,673,675,677,679,681,683,685,687,689
select selected or 691,693,695,697,699

select selected or 701,703,705,707,709
select selected or 711,713,715,717,719,721,723,725,727,729
select selected or 731,733,735,737,739,741,743,745,747,749
select selected or 751,753,755,757,759,761,763,765,767,769
select selected or 771,773,775,777,779,781,783,785,787,789
select selected or 791,793,795,797,799

select selected or 801,803,805,807,809
select selected or 811,813,815,817,819,821,823,825,827,829
select selected or 831,833,835,837,839,841,843,845,847,849
select selected or 851,853,855,857,859,861,863,865,867,869
select selected or 871,873,875,877,879,881,883,885,887,889
select selected or 891,893,895,897,899

select selected or 901,903,905,907,909
select selected or 911,913,915,917,919,921,923,925,927,929
select selected or 931,933,935,937,939,941,943,945,947,949
select selected or 951,953,955,957,959,961,963,965,967,969
select selected or 971,973,975,977,979,981,983,985,987,989
select selected or 991,993,995,997,999

define odd selected

------------------------------------------------------------------
file repsoff.spt
------------------------------------------------------------------
#TURN OFF ALL REPRESENTATIONS FOR SELECTED ATOMS
labels off
monitors off
dots off
wireframe off
backbone off
spacefill off
ribbons off
trace off
strands off
cartoons off

---------------------------------------------------------------------

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: "Francis M. J. Hsieh" <mjhsieh@life.nthu.edu.tw>
Subject: Re: Announce: RasMol
Date: Tue, 19 May 1998 11:40:26 +0800
To: rasmol@dhcp-srv2.oit.umass.edu

At 05:03 AM 1998/5/18 , you wrote:
>5. export current representation as POVRay file
>
>       write povray FILENAME

The povray's camera is at the right place this time. :-)
But it still can't write ribbon view or cartoon view to pov file. Seems that
there are no
object for them.

--
"No, `Eureka' is Greek for `This bath is too hot.'"
                -- Dr. Who

References: <199805190338.LAA02140@sparc.life.nthu.edu.tw>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: Announce: RasMol
Date: Tue, 19 May 1998 14:41:02 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Francis M. J. Hsieh wrote:
> 
> At 05:03 AM 1998/5/18 , you wrote:
> >5. export current representation as POVRay file
> >
> >       write povray FILENAME
> 
> The povray's camera is at the right place this time. :-)
> But it still can't write ribbon view or cartoon view to pov file. Seems that
> there are no
> object for them.

Dear Francis,

Yes your're right, there's no support for 'curved' objects at the
moment, because
RasMol does't store the triangles theese objectes are built of. I hope
to find a way to use some POVRay version 3 special functions to
construct these object. Cartoons and Ribbons are off course important.

	Greetings,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und 
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen        
Germany
phone: +49-551-399654   | fax  : +49-551-393805   
email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Combining 2 molecules correctly oriented into one PDB
Date: Thu, 21 May 1998 16:21:04 -0400
To: "J. J. Stewart" <jstewart@watson.princeton.edu>
Cc: rasmol@dhcp-srv2.oit.umass.edu

At 5/21/98 , you wrote:
>Eric,
>
>I would like to combine two PDB files (antibody and DNA) then show the
>likely orientation for DNA/AB binding.  I can cut and paste the PDB
>files so that both molecules are displayed at the same time, but I
>cannot move only one molecule relative to the other.  Can this be done
>in RasMol?
>
>Thank you in advance.
>
>Jeff Stewart
>Department of Moleular Biology
>Princeton
> 

RasMol cannot, see

http://www.umass.edu/microbio/rasmol/pdbtools.htm

Best way I would know how is with the Swiss PDB Viewer freeware.
It will take you a few hours to get the hang of using it though.
It is a great program and if you want to do this kind of thing more than
once, well worth learning how to use.  (It can easily align two homologous
backbones and save the aligned coordinates, e.g. to show a conformational
change similar to a kinemage in Chime.)

http://www.pdb.bnl.gov/expasy/spdbv/mainpage.html

-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Win32-version of Rasmol 2.6x
Date: Sun, 24 May 1998 19:51:33 +0200
To: Rasmol Mailinglist <rasmol@dhcp-srv2.oit.umass.edu>

Hi all,

anybody out there who has compiled a Win32-version of Rasmol 2.6x??

Or can we expect anything like that in the near future?

I have successfully compiled Rasmol 2.6x on a SGI Indigo2 under Irix 5.???,
but I don´t have a C-Compiler for Windows.

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

-----BEGIN PGP SIGNATURE-----
Version: PGP for Personal Privacy 5.0
Charset: noconv

iQA/AwUBNVixqiPrGHYouWn/EQLa7ACgr2TjKYnCykN5wcBA12HKdJQHCo0AoJYQ
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=JQ9Y
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References: <35685E25.39A32EC@rz.ruhr-uni-bochum.de>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: Win32-version of Rasmol 2.6x
Date: Mon, 25 May 1998 22:34:41 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Marc Saric wrote:
> 
> Hi all,
> 
> anybody out there who has compiled a Win32-version of Rasmol 2.6x??
> 
> Or can we expect anything like that in the near future?
> 

Hi all,

I've found Microsoft Visual C++ for winNT on a Computer in our computing
center, so I hope do produce a binary soon. Nevertheless, a quit trial
to build the executable wasn't successfull, so I think I've to spend
some more time on it!

> I have successfully compiled Rasmol 2.6x on a SGI Indigo2 under Irix 5.???,
> but I don´t have a C-Compiler for Windows.
> 

	greetings,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und 
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen        
Germany
phone: +49-551-399654   | fax  : +49-551-393805   
email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

++++------+------+------+------+------+------+------+------+------+------+
From: Charlie Bond <charlieb@biochem.usyd.edu.au>
Subject: chime problem with center
Date: Tue, 26 May 1998 18:08:07 +1100
To: rasmol@dhcp-srv2.oit.umass.edu

Hi All,
I've written a cgi script which brings up the active site of a selected
protein molecule in a chime window. I have a couple of problems with
this...

1) If I read  the complete PDB file, I can use translate center to get
the centre correctly, but when I rotate the molecule with the mouse, the
centre shifts. If I cut down the size of the molecule to only include,
say, a 10 Angstrom sphere of atoms, this behaviour stops (but this
requires creation of a temporary file which I don't want).

2) Has anyone got 'load pdb inline' to work with chime,not calling a
separate script file, but having the coordinates inline within the
<embed> tag? (As this would cure my problem above).

3) Can I zoom right into an active site automatically? I can get a
certain level of zoom from within the script ro with scale3d, but I can
always increase this using the mouse - I would rather get the maximum
from within the script.

Cheers,
Charlie

References: <35685E25.39A32EC@rz.ruhr-uni-bochum.de>
X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id KAA27440
++++------+------+------+------+------+------+------+------+------+------+
From: Gerard Pujadas <pujadas@argo.urv.es>
Subject: Re: Win32-version of Rasmol 2.6x
Date: Tue, 26 May 1998 16:42:45 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

Hi all too,

>
>Hi all,
>
>I've found Microsoft Visual C++ for winNT on a Computer in our computing
>center, so I hope do produce a binary soon. Nevertheless, a quit trial
>to build the executable wasn't successfull, so I think I've to spend
>some more time on it!
>
>	greetings,
>
>	Arne
>

and what about a PowerMac version?

Best regards !!!

Gerard.

===========================================================================
===  IMPORTANT TELEPHONE/FAX NUMBERS IN THE SPANISH STATE HAVE CHANGED  ===
===========================================================================
DR. GERARD PUJADAS
BIOTECNOLOGIA COMPUTACIONAL
DEPT. BIOQUIMICA I BIOTECNOLOGIA	   E-MAIL: pujadas@quimica.urv.es
UNIV. ROVIRA I VIRGILI                     PHONE: 34-977 559565
PLAÇA IMPERIAL TARRACO 1                   FAX: 34-977 559597
43005 TARRAGONA (CATALONIA)
STATE: SPAIN (EUROPEAN UNION)
===========================================================================

++++------+------+------+------+------+------+------+------+------+------+
From: Keith Rogers <krogers@es.com>
Subject: Re: Win32-version of Rasmol 2.6x
Date: Tue, 26 May 1998 09:33:17 -0600 (MDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Arne wrote:
>I've found Microsoft Visual C++ for winNT on a Computer in our computing
>center, so I hope do produce a binary soon. Nevertheless, a quit trial
>to build the executable wasn't successfull, so I think I've to spend
>some more time on it!

Curious.  I was in a similar situation, recently having a copy of VC++
installed on my NT (4.0) box at work and the first thing I tried doing
with it was compiling RasWin (2.6).  I had no difficulties.  I am by
no means familiar with VC++ or any other Windows/DOS compilers as my
work to date has been largely assembly and some C on unix.  The only
preparation before hitting the compile button was to make sure the
resource list included the correct files.

Keith Rogers

++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: Win32-version of Rasmol 2.6x
Date: Tue, 26 May 1998 21:42:27 +0200 (MET DST)
To: rasmol@dhcp-srv2.oit.umass.edu

> 
>  
> Hi all too, 
>  
> > 
> >Hi all, 
> > 
> >I've found Microsoft Visual C++ for winNT on a Computer in our computing 
> >center, so I hope do produce a binary soon. Nevertheless, a quit trial 
> >to build the executable wasn't successfull, so I think I've to spend 
> >some more time on it! 
> > 
> >	greetings, 
> > 
> >	Arne 
> > 
>  
> and what about a PowerMac version? 

Hi All,

Hm, we've a Mac and a Symatec Compiler in our Computing Center. I think the 
Symatec Compiler will be able to do it's work, it's only me who's only contact
with a mac was about a distance of some meters ... ;-). It was a gray box with
this funny apple symbol -  that's my only experience with mac. But I'll face 
the problem and try to login to build the executable.

	sorry for this,

	Arne

++++------+------+------+------+------+------+------+------+------+------+
From: Tim Maffett <tim@mdli.com>
Subject: Re: chime problem with center
Date: Tue, 26 May 1998 13:10:47 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

At 06:08 PM 5/26/98 +1100, Charlie Bond wrote:
>Hi All,
>I've written a cgi script which brings up the active site of a selected
>protein molecule in a chime window. I have a couple of problems with
>this...
>
>1) If I read  the complete PDB file, I can use translate center to get
>the centre correctly, but when I rotate the molecule with the mouse, the
>centre shifts. If I cut down the size of the molecule to only include,
>say, a 10 Angstrom sphere of atoms, this behaviour stops (but this
>requires creation of a temporary file which I don't want).
>
>2) Has anyone got 'load pdb inline' to work with chime,not calling a
>separate script file, but having the coordinates inline within the
><embed> tag? (As this would cure my problem above).
>

  'load pdb inline' works in the Chime 2.0 beta.

>3) Can I zoom right into an active site automatically? I can get a
>certain level of zoom from within the script ro with scale3d, but I can
>always increase this using the mouse - I would rather get the maximum
>from within the script.
>
>Cheers,
>Charlie
>
>

References: <356A6A57.446B@biochem.usyd.edu.au>
++++------+------+------+------+------+------+------+------+------+------+
From: Kris and/or George <klinger@3-cities.com>
Subject: Re: chime problem with center
Date: Tue, 26 May 1998 20:35:45 -0700
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: rasmol@dhcp-srv2.oit.umass.edu

Charlie,
Interesting observation.  I'll noticed the same behavior, except I thought I
must have been doing something wrong (or else losing my mind).  The center
does shift after rotation.  There must be some center-of-gravity routine
that kicks in when you zoom-in.  I can confirm your observation - the center
does return to an expected place.  Is this perhaps this is due to a bug in
some routine provided in the linking libary or else a complier bug...  I'm
curious too. Any thoughts?
George
===========================================================
George Klinger
Sr. Research Scientist
Pacific Northwest National Laboratory
MS P7-22 POBox 999
Richland, WA 99352
George.Klinger@pnl.gov
(509)372-0448

Charlie Bond wrote:

> Hi All,
> I've written a cgi script which brings up the active site of a selected
> protein molecule in a chime window. I have a couple of problems with
> this...
>
> 1) If I read  the complete PDB file, I can use translate center to get
> the centre correctly, but when I rotate the molecule with the mouse, the
> centre shifts. If I cut down the size of the molecule to only include,
> say, a 10 Angstrom sphere of atoms, this behaviour stops (but this
> requires creation of a temporary file which I don't want).
>
> 2) Has anyone got 'load pdb inline' to work with chime,not calling a
> separate script file, but having the coordinates inline within the
> <embed> tag? (As this would cure my problem above).
>
> 3) Can I zoom right into an active site automatically? I can get a
> certain level of zoom from within the script ro with scale3d, but I can
> always increase this using the mouse - I would rather get the maximum
> from within the script.
>
> Cheers,
> Charlie

References: <356A6A57.446B@biochem.usyd.edu.au>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Centering problems; load pdb inline; scale3d
Date: Wed, 27 May 1998 08:14:00 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

George Klinger and Charlie Bond have been discussing the center of rotation
moving off-center during rotation at high zooms.

As I alluded to in my message of Apr 20, it is my deduction from the
behavior of RasMol and Chime that there is a limited space into which the
molecule must fit.  When you zoom to an off-center moiety, and then rotate,
the other side of the molecule may 'hit the wall' of this limited space,
thereby pushing the center of rotation off-center.   The only solutions I
know to this are to reduce the zoom, or to save a smaller subset of the
atoms into a separate PDB file and use that.

I have not been able to get 'load pdb inline' to work.  I have just sent
Tim Maffett my test example.  If I succeed, I'll post a working example to
this list.  Has anyone else succeeded?

>Charlie Bond wrote:
>> 3) Can I zoom right into an active site automatically? I can get a
>> certain level of zoom from within the script ro with scale3d, but I can
>> always increase this using the mouse - I would rather get the maximum
>> from within the script.

Charlie, please explain in more detail.  What is 'scale3d'?

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <356A6A57.446B@biochem.usyd.edu.au>
++++------+------+------+------+------+------+------+------+------+------+
From: Tim Maffett <tim@mdli.com>
Subject: Re: chime problem with center
Date: Tue, 26 May 1998 22:29:02 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

At 08:35 PM 5/26/98 -0700, you wrote:
>Charlie,
>Interesting observation.  I'll noticed the same behavior, except I thought I
>must have been doing something wrong (or else losing my mind).  The center
>does shift after rotation.  There must be some center-of-gravity routine
>that kicks in when you zoom-in.  I can confirm your observation - the center
>does return to an expected place.  Is this perhaps this is due to a bug in
>some routine provided in the linking libary or else a complier bug...  I'm
>curious too. Any thoughts?
>George

  Chime 2.0 has a couple of features in regard to zooming that 
are new, and one of these is that by default chime will 'center on zooming'.
The point that is centered is by default the center of rotation, but
in Chime can also keep track of a separate zooming center that can be
set using 'translate center <expression>'.  More details on these commands
can be found in the chime manual or I am sure at Eric Martz site.

some relevant commands:

set zoom center true|false
set picking center
translate center <atom expression>

>===========================================================
>George Klinger
>Sr. Research Scientist
>Pacific Northwest National Laboratory
>MS P7-22 POBox 999
>Richland, WA 99352
>George.Klinger@pnl.gov
>(509)372-0448
>
>Charlie Bond wrote:
>
>> Hi All,
>> I've written a cgi script which brings up the active site of a selected
>> protein molecule in a chime window. I have a couple of problems with
>> this...
>>
>> 1) If I read  the complete PDB file, I can use translate center to get
>> the centre correctly, but when I rotate the molecule with the mouse, the
>> centre shifts. If I cut down the size of the molecule to only include,
>> say, a 10 Angstrom sphere of atoms, this behaviour stops (but this
>> requires creation of a temporary file which I don't want).
>>
>> 2) Has anyone got 'load pdb inline' to work with chime,not calling a
>> separate script file, but having the coordinates inline within the
>> <embed> tag? (As this would cure my problem above).
>>
>> 3) Can I zoom right into an active site automatically? I can get a
>> certain level of zoom from within the script ro with scale3d, but I can
>> always increase this using the mouse - I would rather get the maximum
>> from within the script.
>>
>> Cheers,
>> Charlie
>
>
>
>
>

++++------+------+------+------+------+------+------+------+------+------+
From: Keith Rogers <krogers@xmission.com>
Subject: Re: Win32-version of Rasmol 2.6x
Date: Wed, 27 May 1998 11:34:48 -0600 (MDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Regarding me building RasWin from source using Visual C++,

Linton Freeman wrote:
> Would you be willing to share your binary code for the Windows/DOS
> version?

I could in principle, but explaining a difficulty and observation is
in order on my part.

The difficulty - When I wrote I had recently compiled RasWin, I meant
3 months ago.  Since then my disk drive has been completely rebuilt
and so I lost all the files I had.  I also now don't remember just
what I did to get it to compile, only that it wasn't difficult to do.
I could refetch the source and figure out how I complied the program,
but,

The observation - My compiled version behaved no differently than the
executable from the RasMol homepage.  None of the compile time options
I tried (eg optimize execution speed) made any discernable difference.

So, after my disk was rebuilt I just downloaded the program from the
homepage and have been using that.  The only change I made to the
source when I compiled myself was to alter the window parameters so
the placement and size upon program launch was what I wanted.

I guess this is my long-winded way of saying I'm not currently able to
share the binary, and there didn't seem to be any added value to what
I compiled over the executable available from the RasMol homepage.

Keith Rogers

++++------+------+------+------+------+------+------+------+------+------+
From: Linton Freeman <lin@aris.ss.uci.edu>
Subject: Re: Win32-version of Rasmol 2.6x
Date: Wed, 27 May 1998 10:41:41 -0700 (PDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Okay, thanks for the clear statement.  I'll go on using the "official"
version.
Lin

--------------------------------------------------------------------------
Linton C. Freeman                              Phone: Office: 949 824-6698
Institute for Mathematical Behavioral Sciences        Sec.:   949 824-8495
School of Social Sciences  SSPA 2143                  Home:   949 494-6139
University of California                              FAX:    949 824-3733
Irvine, CA 92697-5100                          E-mail: LIN@ARIS.SS.UCI.EDU
  My personal web page is at  "http://eclectic.ss.uci.edu/~lin/lin.html"
---------------------------------------------------------------------------

References: <356A6A57.446B@biochem.usyd.edu.au> <3.0.5.32.19980526222902.009c4840@mind.net>
++++------+------+------+------+------+------+------+------+------+------+
From: Charlie Bond <charlieb@biochem.usyd.edu.au>
Subject: Re: chime problem with center
Date: Thu, 28 May 1998 12:22:23 +1100
To: rasmol@dhcp-srv2.oit.umass.edu

Tim Maffett wrote:
> set using 'translate center <expression>'.  More details on these commands

This was not, however, my problem. I used 'translate center', but find
that while the new centre is preserved, as I rotate the molecule, it
shifts away temporarily. 

To recreate this, load in a large pdb file (a protein), 'translate
center' to somewhere in the molecule and zoom in. When you try to rotate
the molecule you will find the above problem.

> >> 1) If I read  the complete PDB file, I can use translate center to get
> >> the centre correctly, but when I rotate the molecule with the mouse, the
> >> centre shifts. If I cut down the size of the molecule to only include,
> >> say, a 10 Angstrom sphere of atoms, this behaviour stops (but this
> >> requires creation of a temporary file which I don't want).

References: <356A6A57.446B@biochem.usyd.edu.au> <0ETM00031A8A21@pobox1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Charlie Bond <charlieb@biochem.usyd.edu.au>
Subject: Re: Centering problems; load pdb inline; scale3d
Date: Thu, 28 May 1998 12:31:47 +1100
To: rasmol@dhcp-srv2.oit.umass.edu

Eric Martz wrote:
> When you zoom to an off-center moiety, and then rotate,
> the other side of the molecule may 'hit the wall' of this limited space,
> thereby pushing the center of rotation off-center.   The only solutions I
> know to this are to reduce the zoom, or to save a smaller subset of the
> atoms into a separate PDB file and use that.

This would explain, exactly, my problem.

> Charlie, please explain in more detail.  What is 'scale3d'?

It's just a zoom option within the HTML <embed> tag.

>From the MDLI chime FAQ:
http://www.mdli.com/chemscape/chime/chimehelp.html#Dev2

>What are the specific EMBED options allowed by the Chime plug-in?
.
[snip]
.
>scale3D={real value} - Specifies a scaling value (in Angstroms per inch) to be used when a
>     3D structure is displayed. When the same scale3D value is used for multiple Chime structure
>     windows on a page, the viewer can get a feel for the relative size of the structures. 

This works up to a certain level (but values of 1A/" for parts of a
large protein aren't possible).

Cheers,
Charlie

References: <Pine.GSO.3.96.980527111742.15214A-100000@xmission.xmission.com>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: Win32-version of Rasmol 2.6x
Date: Wed, 27 May 1998 20:15:45 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Keith Rogers wrote:

> homepage and have been using that.  The only change I made to the
> source when I compiled myself was to alter the window parameters so
> the placement and size upon program launch was what I wanted.

> I guess this is my long-winded way of saying I'm not currently able to
> share the binary, and there didn't seem to be any added value to what
> I compiled over the executable available from the RasMol homepage.

Of course not, I would be happy with a Windows-version, which remembers it´s
size and position every time at startup! :-))

Beside that -there´s no Rasmol 2.6x-binary at the homepage at the moment
afaik.

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

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++++------+------+------+------+------+------+------+------+------+------+
From: Keith Rogers <krogers@xmission.com>
Subject: Re: Win32-version of Rasmol 2.6x
Date: Thu, 28 May 1998 14:58:44 -0600 (MDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Marc Saric wrote:
> Of course not, I would be happy with a Windows-version, which
> remembers it´s size and position every time at startup! :-))

I'm afraid my modification was not so useful.  I simply replaced the
default window placement parameters with others suitable for my large
monitor.  I, too, would like an executable in which the windows would
remember their size and placement, but I have had no opportunity to
look into how to do that myself, yet.

> Beside that -there´s no Rasmol 2.6x-binary at the homepage at the
> moment afaik.

I was surprised at this comment, so I just checked.  I found a 32 bit
Windows binary in the usual place, by following the "download" links.
To make sure we're talking about the same RasMol homepage, here's the
URL I'm using:

http://klaatu.oit.umass.edu:80/microbio/rasmol/

regards,

Keith Rogers

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Retaining RasMol's window size/placement
Date: Thu, 28 May 1998 16:13:00 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Reminder: shareware which will retain RasMol's windows sizes and placements
is available for both Windows95 and Windows 3.1x, and documented in detail
under 'frequently asked questions'

http://www.umass.edu/microbio/rasmol/faq_em.htm#windows

Also, please don't use the 'klaatu' URL for the RasMol Home Page.  The one
which won't break is below.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: ANN: C4 releases 2 new Chime-based tutorials
Date: Fri, 29 May 1998 22:12:44 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

Greetings Rasmolers,

I invite all members of this list to take a look at our recently released 
Chime-based "Molecular Library" and "Insulin Tutorial" at  
http://c4.cabrillo.cc.ca.us

The Molecular Library contains about 400 'live" molecular models, 
including almost all commonly studied compounds. Once you select a 
compound it is displayed in a viewer window. With the mouse you can 
control:
  - its display style, from wireframe to spacefilling
  - its position and orientation in all 3 dimensions 
  - its size, by zooming in and out on any part of it. 

In the duo-viewer you can use side by side windows to directly compare 
the structures of 2 compounds, such as a pair of enantiomers.  The 
Library is designed to be used in a classroom with a computer projection 
system or over a network or as an individual teacher's or student's 
source of molecular models and images. Any molecular image generated here 
can be copied to the clipboard and pasted into any other software that 
accepts images, such as Word or PowerPoint. 

The Insulin Tutorial uses extensive Chime scripting to examine the 
structure of the protein insulin, dissecting it into two subunits, then 
zooming in on its disulfide bonds and both its alpha helices. The 
tutorial can be used both as a multimedia lecture aid and by students as 
an independent assignment. 

Last month these programs won a Model Showcase Award from the California 
Community College Foundation. The C4 web site was selected by The 
Alchemist's WebPick on 27 March 1998 as an outstanding Chemistry place to 
visit. 

(Reference: 
http://ChemWeb.com/alchem/alchem98/webpicks/wpold/wp_980327_text.html).

They have been used teachers and students at the University of 
California, Santa Cruz and at Cabrillo Community College. 
We hope that you will recommend the insulin tutorial and molecular 
library to your students, that you will link your web pages to it and 
download it for use on your own computers.

This software is produced by C4 (Computers in Chemistry at Cabrillo 
College) and is supported by a grant from the National Science 
Foundation. All C4 software may be used and reproduced without cost, 
provided it is for non-commercial purposes only.

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: load pdb inline
Date: Fri, 29 May 1998 16:23:27 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Recently Charlie Bond started a discussion about the use of 'load pdb
inline' with Chime.
I could not get it to work following the instructions in the Rasmol manual,
and putting the script and inline coordinates in the <embed ...> tag.  I
sent my example to Tim Maffett, who replied that he thinks for Chime, this
only works if the script and inline coordinates are in a separate script
file, not part of the <embed ...> tag script.  I have not had time to test
this, but I pass it along in case anyone else wants to test it and report
results to the rest of us.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <Pine.GSO.3.96.980528145135.24282B-100000@xmission.xmission.com>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: Win32-version of Rasmol 2.6x
Date: Sat, 30 May 1998 01:23:47 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Keith Rogers wrote:

> > Beside that -there´s no Rasmol 2.6x-binary at the homepage at the
> > moment afaik.
> 
> I was surprised at this comment, so I just checked.  I found a 32 bit
> Windows binary in the usual place, by following the "download" links.
> To make sure we're talking about the same RasMol homepage, here's the
> URL I'm using:
> 
> http://klaatu.oit.umass.edu:80/microbio/rasmol/
Well, I haven´t checked that today, but as far as I can see, the newest
version is 2.6b2a or something like this, not the recently anounced 2.6x with
POVRay support and some other improvements (dihedrals output).

See the posting from Arne Mueller.

Maybe I´m wrong here, but I haven´t seen an updated binary for the
Win32-platform.

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

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++++------+------+------+------+------+------+------+------+------+------+
From: "David M. Bourdon" <c680296@showme.missouri.edu>
Date: Mon, 8 Jun 1998 16:30:13 -0500
To: "RasMol" <rasmol@dhcp-srv2.oit.umass.edu>

This is a multi-part message in MIME format.

------=_NextPart_000_0001_01BD92FA.B6839D40
	charset="iso-8859-1"

This may be a silly question but I'm still rather rusty with
RasMol after using it for the first time last week.

How can I locate (and mark) a particular amino acid in a
.pdb structure?

Thanks for your help.

DM Bourdon

David M. Bourdon
Department of Pharmacology
University of Missouri-Columbia
School of Medicine
Columbia, MO 65212, USA
TEL 573-882-1546
FAX 573-884-4558
E-MAIL c680296@showme.missouri.edu
INTERNET www.missouri.edu/~c680296

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	charset="iso-8859-1"

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<HTML>
<HEAD>

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http-equiv=3DContent-Type>
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</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><SPAN class=3D970552721-08061998><FONT color=3D#000000 face=3DArial =
size=3D2>This=20
may be a silly question but I'm still rather rusty with RasMol after =
using it=20
for the first time last week.</FONT></SPAN></DIV>
<DIV><SPAN class=3D970552721-08061998><FONT color=3D#000000 face=3DArial =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D970552721-08061998><FONT color=3D#000000 face=3DArial =
size=3D2>How=20
can I locate (and mark) a particular amino acid in a .pdb=20
structure?</FONT></SPAN></DIV>
<DIV><SPAN class=3D970552721-08061998><FONT color=3D#000000 face=3DArial =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D970552721-08061998><FONT color=3D#000000 face=3DArial =
size=3D2>Thanks=20
for your help.</FONT></SPAN></DIV>
<DIV><SPAN class=3D970552721-08061998><FONT color=3D#000000 face=3DArial =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D970552721-08061998><FONT color=3D#000000 face=3DArial =
size=3D2>DM=20
Bourdon</FONT></SPAN></DIV>
<DIV><SPAN class=3D970552721-08061998><FONT color=3D#000000 face=3DArial =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D970552721-08061998><FONT color=3D#000000 face=3DArial =
size=3D2><FONT=20
size=3D1>David M. Bourdon <BR>Department of Pharmacology <BR>University =
of=20
Missouri-Columbia <BR>School of Medicine <BR>Columbia, MO 65212, USA =
<BR>TEL=20
573-882-1546 <BR>FAX 573-884-4558 <BR>E-MAIL c680296@showme.missouri.edu =

<BR>INTERNET www.missouri.edu/~c680296 <BR></FONT>&nbsp;=20
</FONT></SPAN></DIV></BODY></HTML>

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References: <000001bd9324$9f59a540$2e3782a1@MU.showme.missouri.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: "Francis M.J. Hsieh" <mjhsieh@life.nthu.edu.tw>
Subject: Re: David M. Bourdon's mail
0500
To: c680296@showme.missouri.edu, rasmol@dhcp-srv2.oit.umass.edu

On Mon, Jun 08, 1998 at 04:30:13PM -0500, David M. Bourdon wrote:
> This may be a silly question but I'm still rather rusty with
> RasMol after using it for the first time last week.
> How can I locate (and mark) a particular amino acid in a
> .pdb structure?

Dear DM;
	select a particular amino acid and label.

for example; if you want to label the VAL283
(you can get this information by "show sequence" command)
you can:
RasMol> select 283
7 atoms selected!
RasMol> spacefill   ----> only these 7 atoms will be presented as spacefill
RasMol> label VAL

ps. There are tons of documents in Eric's rasMol homepage, it is much faster
    to find answers there.
-- 
Francis M. J. Hsieh      | Email:   mjhsieh@life.nthu.edu.tw
Life Science Department, | Webpage: http://www.life.nthu.edu.tw/~mjhsieh/
National Tsing Hua Univ, | Voice:   +886 3 5715131 ext 3482
HsinChu, Taiwan Republic | 	    +886 3 5715649

++++------+------+------+------+------+------+------+------+------+------+
From: Stuart Green <S.M.Green@chemistry.leeds.ac.uk>
Subject: Rasmol, DDE, Tcl
Date: Thu, 11 Jun 1998 17:44:59 +0100 (BST)
To: rasmol@dhcp-srv2.oit.umass.edu

Rasmol people,

Has anyone used the Windows DDE interface to control Rasmol?

I've tried to do this using the 'dde' command in wish8.1
eg.

  dde execute RasWin System cpk

Unfortunately, this and other communication hang wish.

Any help greatly appreciated.

Cheers,

Stuart

-- 
Stuart M. Green                               S.M.Green@chem.leeds.ac.uk
School of Chemistry
University of Leeds                           Tel +44 113 233 6596
Leeds, LS2 9JT, England                       Fax +44 113 233 6563

X-ROUTED: Fri, 12 Jun 1998 10:30:14 -0300
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++++------+------+------+------+------+------+------+------+------+------+
From: ciearg <ciearg@ieducativa.com.ar>
Subject: Chime Problem
Date: Fri, 12 Jun 1998 10:27:14 -0300
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Colleagues:

I have been used Chime in my web pages over a Linux platform. Now I have translated my pages to a Windows NT Server.
For an extraneos reason when I try to see the page with Netscape Communicator 4.03 on line, the plug-in don´t work. It tries
to download an .exe file. (?????)
Do I must set anything in my server?
Chime only works when I see my pages with Internet Explorer 4.0.
Why does it happen?

Anybody who can help me, THANKS THANKS THANKS!!!

Hernán Chiapella
Cie Argentina
Argentina            Hernán Chiapella
programador de Internet Educativa
     ciearg@ieducativa.com.ar

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Re: How to access Chime <embed> options from a button?
Date: Mon, 15 Jun 1998 11:49:42 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

OK, I've figured out the answers to several of my questions.

Although it is not documented in the Rasmol v2.6b2 or Chime 0.99 manuals, 
I found the following morsel within the Chime 2.0 beta documentation 
entitled Chime Embed Tags Options Reference. 

"startanim
 --------- 
Set to true if you want an animation in a concatenated XYZ file to begin 
immediately. 
If false, you can start the animation using the RasMol script command 
'animation on'. "

Although it doesn't seem to be documented in the Rasmol v2.6b2 or Chime 
0.99 manuals, 'animation on' and 'animation off' both work, even with 
Chime 1.0! This, coupled with the Chime 2.0-only "anim frame" script 
command, which allows advancing forward and backward 1 frame at a time, 
are what I was looking for.

My remaining questions:

1. I still would like to know if there is any way of directly accessing 
<embed> options via a button to change the state of an existing Chime 
model (plug-in) without zapping and reloading the model (and losing its 
display mode and position). I've only used ButtonCallback to stream 
Rasmol scripts to a model, so I'm not sure if it can do this or not.

2. Can Chime obtain charge information (for coloring purposes) directly 
from either a Mopac file (assuming the z matrix has a charge value for 
each atom) or an .xyz file (again, assuming the values are there), or do 
I have to hand-code each value using the 'set charge' script command? 

3. (to Brian or Tim) Chime 2.0 is really impressive, do you have any idea 
when the Mac version will be available? :-)

thanks,
Slaton Lipscomb
C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

>I am putting together a relatively simple web viewer for .xyz animations made
>from MOPAC output. I want to use buttons to start and pause/stop the 
animations
>without having to reload (and therefore reset the orientation and display 
mode of)
>the model, and without requiring the use of the Chime contextual menu.
>
>Chime has several documented <embed> options for manipulation of .xyz 
>animations ( startanim, animfps, animmode, AnimFrameCallback ). 
>
>However, as far as I know, Chime (I am only using 1.0 - still waiting for 2.0 
for
>Mac) only supports Rasmol and CSML scripting with buttons. There doesn't 
>appear to be any way of directly accessing the <embed> options from any kind 
of 
>button. This is unfortunate. True, for most purposes, such as changing the 
visual
>display of a model, all of the embed options can be replicated with Rasmol 
scripts. 
>However since Rasmol does not read .xyz files,  it has no animation-control
>commands.
>
>Have I overlooked something here? Or is there a feature in Chime 2.0 that 
will let
>me communicate directly between a button and a Chime model without using
>Rasmol scripts (perhaps using Javascript)?

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: How to access Chime <embed> options from a button?
Date: Mon, 15 Jun 1998 02:58:02 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

Greetings,

I am putting together a relatively simple web viewer for .xyz animations 
made from MOPAC output. I want to use buttons to start and pause/stop the 
animations without having to reload (and therefore reset the orientation 
and display mode of) the model, and without requiring the use of the 
Chime contextual menu.

Chime has several documented <embed> options for manipulation of .xyz 
animations ( startanim, animfps, animmode, AnimFrameCallback ). 

However, as far as I know, Chime (I am only using 1.0 - still waiting for 
2.0 for Mac) only supports Rasmol and CSML scripting with buttons. There 
doesn't appear to be any way of directly accessing the <embed> options 
from any kind of button. This is unfortunate. True, for most purposes, 
such as changing the visual display of a model, all of the embed options 
can be replicated with Rasmol scripts. However since Rasmol does not read 
.xyz files,  it has no animation-control commands.

Have I overlooked something here? Or is there a feature in Chime 2.0 that 
will let me communicate directly between a button and a Chime model 
without using Rasmol scripts (perhaps using Javascript)?

thanks,
Slaton Lipscomb
C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

References: <18484819705984@surfnetusa.com>
++++------+------+------+------+------+------+------+------+------+------+
From: Thomas Atkins <tsa01@csufresno.edu>
Subject: Re: How to access Chime <embed> options from a button?
Date: Tue, 16 Jun 1998 09:31:28 -0800
To: rasmol@dhcp-srv2.oit.umass.edu

Please take me off the list server for the summer.

Thanks Thomas Atkins

        "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Tim Maffett <tim@mdli.com>
Subject: Re: How to access Chime <embed> options from a button?
Date: Tue, 16 Jun 1998 16:15:43 -0700
To: rasmol@dhcp-srv2.oit.umass.edu,

At 11:49 AM 6/15/98 -0800, slaton@surfnetusa.com wrote:
>OK, I've figured out the answers to several of my questions.
>
>Although it is not documented in the Rasmol v2.6b2 or Chime 0.99 manuals, 
>I found the following morsel within the Chime 2.0 beta documentation 
>entitled Chime Embed Tags Options Reference. 
>
>"startanim
> --------- 
>Set to true if you want an animation in a concatenated XYZ file to begin 
>immediately. 
>If false, you can start the animation using the RasMol script command 
>'animation on'. "
>
>Although it doesn't seem to be documented in the Rasmol v2.6b2 or Chime 
>0.99 manuals, 'animation on' and 'animation off' both work, even with 
>Chime 1.0! This, coupled with the Chime 2.0-only "anim frame" script 
>command, which allows advancing forward and backward 1 frame at a time, 
>are what I was looking for.
>
>My remaining questions:
>
>1. I still would like to know if there is any way of directly accessing 
><embed> options via a button to change the state of an existing Chime 
>model (plug-in) without zapping and reloading the model (and losing its 
>display mode and position). I've only used ButtonCallback to stream 
>Rasmol scripts to a model, so I'm not sure if it can do this or not.
>

  Embed tag buttons can send chime/rasmol scripts to other chime
plugin's, changing then in a variety of ways, without causing
any reload of molecule, etc.  All embed tag options which affect
the 3D part of chime should be available in the chime/rasmol scripting
language in Chime 2.0.
  As always, Eric Martz, among others, has examples of many of
these things.

>2. Can Chime obtain charge information (for coloring purposes) directly 
>from either a Mopac file (assuming the z matrix has a charge value for 
>each atom) or an .xyz file (again, assuming the values are there), or do 
>I have to hand-code each value using the 'set charge' script command? 
>

  Chime 2.0 has extensive capabilities in regards to creating 
surfaces with charges mapped using different ways..
  see the "select->display list" sub menus for UI work.
There are a extensive set of new commands which control loading
of surfaces from external files, etc.  I would hope these are
documented somewhere, but I suspect you may be able to 
glean some of the info from the chime 2.0 examples.
  (do "select->display list->create molecular surface" to create
	a surface)
and then "select->display list->color->...." for various ways
to color it (with electrostatic info or lipophilic potenial).
  Chime 2.0 can use supplied charge data from pdb file, or
compute it in several ways (for small molecules, gasteiger, 
or charmm or kollman for larger molecules (ie. proteins)

here are a few of the chime 2.0 commands in regards to charge, there
are more, hopefully doc'ed somewhere on the website...):

  set charge function none|gasteiger|kollman|charmm
  
  set kollman sprout true|false 

    toggles automatic sprouting of hydrogens on proteins for
    kollman calcs.  

  calculate charge true|false|refresh

    true - set "calc of charges" flag
    false - set "calc of charges" flag to false, which allows
      you to force chime to use the pdb file "atom temp" values
    refresh - causes the actual running of the charge calculations

  Has anyone ever looked at the lipophilicity coloring that
Chime 2.0 can do ?  This can be pretty neat as well pdb files
with ligands doc'ing, etc.

>3. (to Brian or Tim) Chime 2.0 is really impressive, do you have any idea 
>when the Mac version will be available? :-)
>

  This is getting very close, and we Chime 2.0 for the mac is
currently undergoing internal beta testing, and working quite
well.  Sometime in july I would suspect it will be available...
but I don't work in that group currently, so I am not an authority
on this by any means...

-tim

>
>thanks,
>Slaton Lipscomb
>C4: Computers in Chemistry at Cabrillo College
>http://c4.cabrillo.cc.ca.us/
>
>>I am putting together a relatively simple web viewer for .xyz animations
made
>>from MOPAC output. I want to use buttons to start and pause/stop the 
>animations
>>without having to reload (and therefore reset the orientation and display 
>mode of)
>>the model, and without requiring the use of the Chime contextual menu.
>>
>>Chime has several documented <embed> options for manipulation of .xyz 
>>animations ( startanim, animfps, animmode, AnimFrameCallback ). 
>>
>>However, as far as I know, Chime (I am only using 1.0 - still waiting for
2.0 
>for
>>Mac) only supports Rasmol and CSML scripting with buttons. There doesn't 
>>appear to be any way of directly accessing the <embed> options from any
kind 
>of 
>>button. This is unfortunate. True, for most purposes, such as changing the 
>visual
>>display of a model, all of the embed options can be replicated with Rasmol 
>scripts. 
>>However since Rasmol does not read .xyz files,  it has no animation-control
>>commands.
>>
>>Have I overlooked something here? Or is there a feature in Chime 2.0 that 
>will let
>>me communicate directly between a button and a Chime model without using
>>Rasmol scripts (perhaps using Javascript)?
>
>

++++------+------+------+------+------+------+------+------+------+------+
From: "Fernando Gabriel Ranea  " <fgranea@microb.ffyb.uba.ar>
Subject: Molecules in PDB and MOL Format
Date: Tue, 16 Jun 1998 11:28:45 ARG
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Rasmolers:

	My name is Fernando G. Ranea and I'm a student in Biochemyst at
Facultad de Farmacia y Bioquimica (Universidad de Buenos Aires-Argentina).
I'm bulding a Microbiological Web Site called Microbiologia! (outside) but
actually is wrotte in spanish. However, there is a section that it contains
more than 200 molecules in PDB and MOL format. They are compressed in ZIP
format for PC. Free to download and use them with RasMol and/or Swiss PDB
Viewer.
	The molecules were builded using WebLab Viewer Pro 3.0 and Swiss PDB
Viewer 3.0. The configuration and ring numeration are based in The Merck Index
12th Edition and The Chemical Abstracts. Except for the alfa-helix and beta-
sheet that was removed of other proteins. For DNA and peptidic sequences I've
used the MOL-MOL software like "Gold Standard".
	This section contains:

	L-aminoacids
	Antimicrobials Agents (penicillins, cephalosporins, macrolides, etc)
	DNA molecules and nucleotids
	LPS RE and Lipid A
	E. coli ans S. aureus peptidoglican

	Moreover, there is a Virtual Reality 2.0 section that contains 3D models
of bacterias, virus and molecules. This section contains a phage T4, a
adenovirus, a DNA and Lipid A molecule, etc.

	If you find some wrong configuration in some molecule (or all of them)
please tell me. This web site is not receiving neither grants nor susbsidies
because is a personal site.

Microbiologia! (outside): http://www.geocities.com/CapeCanaveral/Lab/7305

PDB and MOL Files: Molecular Insanity Section (.../7305/moleculas.html)

VRML 2.0: Virtual Insanity Section (.../7305/virtual.html)

	Regards,

Fernando Gabriel Ranea 
fgranea@microb.ffyb.uba.ar

++++------+------+------+------+------+------+------+------+------+------+
From: "Nancy O. Manning" <oeder@pdb.pdb.bnl.gov>
Subject: Latest PDB Quarterly Newsletter Released
Date: Mon, 22 Jun 1998 12:28:44 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

The April 1998 PDB Quarterly Newsletter is now available on-line from
the PDB Home Page, http://www.pdb.bnl.gov.

It is in Adobe pdf, postscript, rtf, and ASCII text format.

You can also get it from our anonymous ftp server, ftp.pdb.bnl.gov, in
the directory newsletter/newsletter98apr/.

We have sent the text version to those subscribed to the electronic
newsletter mailing list.  The printed copies will be sent out as soon as
they are received from the printer.

If you have any suggestions for future articles, or wish to contribute
one yourself, please send me e-mail.

Best regards,
Nancy

-- 
_______________________________________________________________________

 Nancy Oeder Manning                  Protein Data Bank
 Head User Support                    Brookhaven National Laboratory
 oeder@bnl.gov                        Biology Department, Bldg. 463
 (516) 344-5744 phone                 P.O. Box 5000
 (516) 344-5751 FAX                   Upton, NY 11973-5000   USA
_______________________________________________________________________

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: PDB Lite!
Date: Mon, 22 Jun 1998 11:22:40 -0400
To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu

I recently met Joel Sussman, Head of the Protein Data Bank at Brookhaven
National Laboratory, for the first time. My concerns about the difficulties
encountered by the general scientific public in using the 3DB Browser led
him invite me to spend 9 days at BNL, during which I had the considerable
pleasure of working closely with Jaime Prilusky to develop an alternative
search interface called "PDB Lite".  Prilusky earlier developed the 3DB
Browser and its powerful search engine, which he continues to enhance and
refine. PDB Lite is designed for use by students, educators, and occasional
users who are nonspecialists.  It offers less power and flexibility and is
thoroughly documented in nontechnical language.  It has fewer links on the
final 'View/Save/Analyze' page (parallel to the 3DB Atlas page) but more
clearly explains what each link offers.

A short overview of the origins and limitations of 3D structural data
(X-ray crystal diffraction or NMR) has been provided (press the [?] button
to the right of the PDB Lite first page title), tho the section on NMR is
weak and I am in the process of revising it with help from my colleague
Lynmarie Thompson.

During the same visit I also wrote a molecule viewing page using Chime
which is intentionally kept simple so it will run on all versions of Chime
(version 1 for Win3.1, Win95, Macintosh, or version 0.9e for SGI).  Once
you install Chime ( www.mdli.com ) you can view any molecule immediately
thru the PDB Lite or 3DB Browser interfaces.

Detailed instructions have been provided for saving a PDB file on a Win95
system, where the default filename is now the PDB ID code instead of
'send-pdb' (thanks to Jaime's creativity and perseverence).

I am continuing to work on PDB Lite and fill in its known deficiencies
(instructions for Win3.1 and Macintosh download, better documentation of
NMR methodology, etc.) If you have other suggestions, please direct them to
me. PDB Lite is available at www.pdb.bnl.gov by clicking on the link "Find,
View, Download Macromolecules with PDB Lite".

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: "Andreas Bohne" <A.Bohne@dkfz-heidelberg.de>
Subject: RasMol26 <---> Linux
Date: Wed, 24 Jun 1998 09:01:57 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Dear List,

who of you have any idea who to solve the problem i am decribing here:
> make
gcc -O2 -fno-strength-reduce     -I/usr/X11R6/include -I/include  -Dlinux
-D__i386__ -D_POSIX_SOURCE -D_BSD_SOURCE -D_SVID_SOURCE -DX_LOCALE
  -DFUNCPROTO=15 -DNARROWPROTO  -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\"
-DEIGHTBIT   -c rasmol.c -o rasmol.o
rasmol.c: In function `FetchCharacter':
rasmol.c:501: `WaitSet' has an incomplete type
rasmol.c:507: warning: passing arg 2 of `select' from incompatible pointer type
rasmol.c:507: warning: passing arg 3 of `select' from incompatible pointer type
rasmol.c:507: warning: passing arg 4 of `select' from incompatible pointer type
rasmol.c: At top level:
rasmol.c:114: storage size of `OrigWaitSet' isn't known
rasmol.c:115: storage size of `WaitSet' isn't known
make: *** [rasmol.o] Error 1

Line 114 ff in rasmol.c
static struct fd_set OrigWaitSet;
static struct fd_set WaitSet;

fd_set is defined in:
/sys/types.h

	/linux/types.h
	typedef __kernel_fd_set         fd_set;

		/linux/posix_types.htypedef struct {
        		unsigned long fds_bits [__FDSET_LONGS];
		} __kernel_fd_set;

Any idea?????

Greetings Andreas

-- 
+---------------------------------------------------
| Dipl.-Inform.			
| Andreas Bohne			
| DKFZ-Heidelberg
| Zentrale Spektroskopie	Raum: D136b
| Im Neuenheimer Feld 280	Tel: 06221 / 42-4541
| D-69120 Heidelberg 		Fax: 06221 / 42-2995

References: <9806240901.ZM13234@zsins1.inet.dkfz-heidelberg.de>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: RasMol26 <---> Linux
Date: Wed, 24 Jun 1998 16:27:50 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Andreas Bohne wrote:
> 
> Dear List,
> 
> who of you have any idea who to solve the problem i am decribing here:
> > make
> gcc -O2 -fno-strength-reduce     -I/usr/X11R6/include -I/include  -Dlinux
> -D__i386__ -D_POSIX_SOURCE -D_BSD_SOURCE -D_SVID_SOURCE -DX_LOCALE
>   -DFUNCPROTO=15 -DNARROWPROTO  -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\"
> -DEIGHTBIT   -c rasmol.c -o rasmol.o
> rasmol.c: In function `FetchCharacter':
> rasmol.c:501: `WaitSet' has an incomplete type
> rasmol.c:507: warning: passing arg 2 of `select' from incompatible pointer type
> rasmol.c:507: warning: passing arg 3 of `select' from incompatible pointer type
> rasmol.c:507: warning: passing arg 4 of `select' from incompatible pointer type
> rasmol.c: At top level:
> rasmol.c:114: storage size of `OrigWaitSet' isn't known
> rasmol.c:115: storage size of `WaitSet' isn't known
> make: *** [rasmol.o] Error 1
> 
> Line 114 ff in rasmol.c
> static struct fd_set OrigWaitSet;
> static struct fd_set WaitSet;
> 
> fd_set is defined in:
> /sys/types.h
> 
>         /linux/types.h
>         typedef __kernel_fd_set         fd_set;
> 
>                 /linux/posix_types.htypedef struct {
>                         unsigned long fds_bits [__FDSET_LONGS];
>                 } __kernel_fd_set;
> 
> Any idea?????
> 
> Greetings Andreas
> 
> --
> +---------------------------------------------------
> | Dipl.-Inform.
> | Andreas Bohne
> | DKFZ-Heidelberg
> | Zentrale Spektroskopie        Raum: D136b
> | Im Neuenheimer Feld 280       Tel: 06221 / 42-4541
> | D-69120 Heidelberg            Fax: 06221 / 42-2995

Hi, 

get RasMol2.6bx1 from

ftp://nexus.roko.goe.net/pub/rasmol/

and see the readme file, fd_set is allready a structure. See the file
rasmol.h of RasMol2.6bx1 for details.

	Greetings,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen
Germany
phone: +49-551-399654   | fax  : +49-551-393805
email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

        "Re: RasMol26 <---> Linux" (Jun 24,  4:27pm)
References: <9806240901.ZM13234@zsins1.inet.dkfz-heidelberg.de> 
	<35912906.7952578B@gwdg.de>
	boundary="PART-BOUNDARY=.19806250808.ZM15329.inet.dkfz-heidelberg.de"
++++------+------+------+------+------+------+------+------+------+------+
From: "Andreas Bohne" <A.Bohne@dkfz-heidelberg.de>
Subject: Re: RasMol26 <---> Linux
Date: Thu, 25 Jun 1998 08:08:14 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

--PART-BOUNDARY=.19806250808.ZM15329.inet.dkfz-heidelberg.de
Content-Description: Text
X-Zm-Decoding-Hint: mimencode -q -u 

 Dear List,

thanks for the help. Here is a summery of the problem and who to solve:

If you see this on a newer Linux-system while compiling:
> > rasmol.c: At top level:
> > rasmol.c:114: storage size of `OrigWaitSet' isn't known
> > rasmol.c:115: storage size of `WaitSet' isn't known
> > make: *** [rasmol.o] Error 1

1) Get RasMol2.6bx1 from
   ftp://nexus.roko.goe.net/pub/rasmol/

2) Edit rasmol.h

   /* define =B4USE_FD_SET_TYPE=B4 if you get compilations  */
   /* errors in =B4rasmol.c=B4 claiming about =B4WaitSet=B4     */
   /* and OrigWaitSet=B4 (happens on newer linux systems) */
   #define USE_FD_SET_TYPE

4) xmkmf and then a make ....

Bye Andreas

-- =

+---------------------------------------------------
| Dipl.-Inform.			=

| Andreas Bohne			=

| DKFZ-Heidelberg
| Zentrale Spektroskopie	Raum: D136b
| Im Neuenheimer Feld 280	Tel: 06221 / 42-4541
| D-69120 Heidelberg 		Fax: 06221 / 42-2995

--PART-BOUNDARY=.19806250808.ZM15329.inet.dkfz-heidelberg.de--

        "Re: RasMol26 <---> Linux" (Jun 25,  8:08am)
References: <9806240901.ZM13234@zsins1.inet.dkfz-heidelberg.de> 
	<35912906.7952578B@gwdg.de> 
++++------+------+------+------+------+------+------+------+------+------+
From: "Andreas Bohne" <A.Bohne@dkfz-heidelberg.de>
Subject: Re: RasMol26 <---> script
Date: Thu, 25 Jun 1998 11:02:06 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Dear List,

while writing a scrit to generate files for a multigif file I get into
problems.

script:

Set Write on
#Group Colours
rotate x 10
rotate y 10
rotate z 10
refresh
save gif ras00.gif

rotate x 10
rotate y 10
rotate z 10
refresh
save gif ras01.gif

#...

rotate x 10
rotate y 10
rotate z 10
refresh
save gif ras35.gif

problem:

andreas> rasmol cpex.pdb -script ras.scr
RasMol Molecular Renderer
Roger Sayle, August 1995
Arne Mueller, Mai 1998
Version 2.6x1
[8bit version]

Secondary Structure . No Assignment
Number of Groups .... 38
Number of Atoms ..... 899
Number of Bonds ..... 935

RasMol>
Set Write on
          ^
"ras.scr",line 1: Command disabled in script file!
save gif ras00.gif
^
"ras.scr",line 7: Command disabled in script file!
save gif ras01.gif
^
"ras.scr",line 13: Command disabled in script file!
save gif ras35.gif
^
"ras.scr",line 21: Command disabled in script file!

What to do???

Greetings Andreas

-- 
+---------------------------------------------------
| Dipl.-Inform.			
| Andreas Bohne			
| DKFZ-Heidelberg
| Zentrale Spektroskopie	Raum: D136b
| Im Neuenheimer Feld 280	Tel: 06221 / 42-4541
| D-69120 Heidelberg 		Fax: 06221 / 42-2995

X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id GAA23236
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: enabeling "write in scripts" 
Date: Thu, 25 Jun 1998 12:06:48 +0200
To: Rasmol Mailinglist <rasmol@dhcp-srv2.oit.umass.edu>

Dear all,

here´s a good tip from the "release.txt" file of RasMol2.6b.
You´ve to type in the command "set write on" on the commandline
ONLY - this is the sense of this command...

...
[4.3]  Controlling Save/Write in Scripts
One of the unpopular changes implemented in RasMol between versions 
2.4 and 2.5 was the disabling of save and write commands from 
within RasMol script files.  With the increasing use of RasMol in 
conjunction with the Internet, the ability to generate/overwrite 
files was regarded as a security hazards.  Many sites now exchange 
RasMol script files that could potentially overwrite system files
and alter acess restrictions.  To prevent such problems, RasMol v2.5 
disallowed the use of save and write commands within scripts.  
However, this has prevented the use of script files in generating 
animated sequences of images.  The proposed solution to this problem 
is the addition of the RasMol "set write <boolean>" command.  This 
command enables (and disables) the use of "save" and "write" in 
scripts, but may only be executed from the command line.  By default, 
this value is "false", prohibiting the generation of files in any 
scripts executed at start-up (such as those launched from a WWW 
browser such as Mosaic or NetScape).  However, animators may start 
up RasMol interactively, type "set write on" and then execute a 
script to generate each frame using the "source" command.
...
	greetings,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und 
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen        
Germany
phone: +49-551-399654   | fax  : +49-551-393805   
email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

++++------+------+------+------+------+------+------+------+------+------+
From: "Wayne M. Barnes" <wayne@barnes1.wustl.edu>
Subject: No suitable display !
Date: Thu, 25 Jun 1998 11:37:19 -0500 (CDT)
To: rasmol@dhcp-srv2.oit.umass.edu

This message cannot be resent again unless its body is slightly modified.

Dear Rasmollers,

    I am having trouble getting rasmol (unix; FreeBSD) to serve my PC
(XWin32; Windows95) with an
xwindow, even though things are properly set up for other programs
to do so (see some screen lines below).  

--------------------------------------------------------
wayne@barnes1:/home/wayne>setenv DISPLAY barnes3:0
wayne@barnes1:/home/wayne>xterm

    [ an xterm window pops up fine, here.]

wayne@barnes1:/home/wayne>surf    [this starts Netscape.]

    [ netscape comes up fine, here. ]

wayne@barnes1:/home/wayne>
wayne@barnes1:/home/wayne>rasmol
RasMol Molecular Renderer
Roger Sayle, August 1995
Version 2.6
[8bit version]

No suitable display detected!
RasMol> exit
------------------------------------------------------

  I have found some discussion similar to this problem on the 
mailing list:

>I've just tried this. You should find that normally you get a "No
>suitable display detected!" and with -nodisplay, a "Display window
>disabled!".  After both of these warnings, you should still get the
>RasMol command line and this will allow you to generate 24bit/pixel
>images on any UNIX machine.

    I notice in the mailing list history that this advice is enough 
for some people, but I wonder if I could have some more clues.  What 
command(s) should I then give on the rasmol command line
to get a window to pop up?  I have no window showing at all!

     Rasmol works fine if I am on a console at the FreeBSD unix 
machine, but I would like to to be able to broadcast to larger 
monitors on Windows95 machines.  Also, I know someone who has a 
similar problem with an astronomy program, and I am hoping someone 
recognizes that there is a simple cure.  

    Thank you,

Wayne M. Barnes           wayne@barnes1.wustl.edu
Washington University Medical School
Dept. Biochemistry 8231   314.362.3351
660 S. Euclid Ave, St. Louis, MO 63110 USA

References: <199806251637.LAA01123@barnes1.wustl.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: No suitable display !
Date: Thu, 25 Jun 1998 19:05:04 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Hi All,

Wayne M. Barnes wrote:
> 
> This message cannot be resent again unless its body is slightly modified.
> 
> Dear Rasmollers,
> 
>     I am having trouble getting rasmol (unix; FreeBSD) to serve my PC
> (XWin32; Windows95) with an
> xwindow, even though things are properly set up for other programs
> to do so (see some screen lines below).
> wayne@barnes1:/home/wayne>rasmol
> RasMol Molecular Renderer
> Roger Sayle, August 1995
> Version 2.6
> [8bit version]
> 
> No suitable display detected!
...
 
>     I notice in the mailing list history that this advice is enough
> for some people, but I wonder if I could have some more clues.  What
> command(s) should I then give on the rasmol command line
> to get a window to pop up?  I have no window showing at all!
> 
>      Rasmol works fine if I am on a console at the FreeBSD unix
> machine, but I would like to to be able to broadcast to larger
> monitors on Windows95 machines.  

Hm, I think rotating the molecule on a remote computer and
putting the Display on your local screen is is allways the 
slowest solution ...

> Also, I know someone who has a
> similar problem with an astronomy program, and I am hoping someone
> recognizes that there is a simple cure.

I've now good idea at the moment, but maybe your X-Server 
running on your win95-machine doesn't offer an 8 bit dsiplay.
Try to find out what color-depth your win95-XServer provides. 
You can do this after exporting the Display to your win95
mashine with:

 xdpyinfo   

in an xterm. 

I get something like this in the first lines of the output:
[...]
supported pixmap formats:
    depth 1, bits_per_pixel 1, scanline_pad 32
    depth 24, bits_per_pixel 32, scanline_pad 32 
[...]

What means that I've a colordepth of 1 or 24 bits (with
1 or 32bits used by the XServer for each pixel).

I don't know how your win95-Xserver behaves about this - 
but It'll be interesting. When running 8bit-RasMol on
your BSD-machine your XServer has to provide 8 bit!

	good luck,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen
Germany
phone: +49-551-399654   | fax  : +49-551-393805
email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

From July 1, 1998:
++++------+------+------+------+------+------+------+------+------+------+
From: "Jesus M. Sanz" <jmsanz@umh.es>
Subject: On-line problems
Date: Thu, 02 Jul 1998 19:20:11 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Dear ChimeUsers,

Sorry if this is already an old one. I have just finished (with a
great effort) a WWW page including the visualization of pdb files using Chime.
Until now, the page has worked properly for my students, 
but now I am trying to publish it
so that it becomes available for the rest of the world. 
However, when accessed through Internet everything becomes a
mess (the pdb files are not visualized-instead, they are automatically
saved, and there are also many other errors). The plug-in seems to be properly
installed, since everything is fine when I load the page directly from
the hard disk.
Is there anything I am missing that is necessary to publish the page?

Thank you very much in advance

Prof. Jesus Sanz

--------------------------------------------------------------------------
Prof. Jesus M. Sanz				Tel:(34) 966 658 761
Dep. Bioquimica y Biologia Molecular		Fax:(34) 966 658 780
Universidad Miguel Hernandez			E-mail: jmsanz@umh.es
c/ Monovar s/n, Poligono Carrus, ELCHE, 03206-Alicante, SPAIN
       "Asombrarse es la esencia de la vida"   M. C. Escher
--------------------------------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: Warren Gallagher <wgallagh@uwec.edu>
Subject: Re: On-line problems
Date: Thu, 2 Jul 1998 12:50:23 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

2. July, 1998

Re:
>>Sorry if this is already an old one. I have just finished (with a
>great effort) a WWW page including the visualization of pdb files using Chime.
>Until now, the page has worked properly for my students,
>but now I am trying to publish it
>so that it becomes available for the rest of the world.
>However, when accessed through Internet everything becomes a
>mess (the pdb files are not visualized-instead, they are automatically
>saved, and there are also many other errors). The plug-in seems to be properly
>installed, since everything is fine when I load the page directly from
>the hard disk.
>Is there anything I am missing that is necessary to publish the page?
>

Be sure that your web server is configured to map the ".pdb" extension to
the MIME type "chemical/x-pdb"

___________________________________________________________________
 Warren Gallagher
  Associate Professor
  Department of Chemistry
  University of Wisconsin-Eau Claire
  Eau Claire  WI  54702-4004
  E-mail: wgallagh@uwec.edu
  TEL:    (715) 836-5388
  FAX:    (715) 836-4979
___________________________________________________________________

                                         

++++------+------+------+------+------+------+------+------+------+------+
From: "Tamas Gunda" <tamasgunda@tigris.klte.hu>
Subject: Re: On-line problems
Date: Fri, 3 Jul 1998 11:33:26 +1
To: rasmol@dhcp-srv2.oit.umass.edu

Jesus Sanz wrote:

>
> Dear ChimeUsers,
> 
> Sorry if this is already an old one. I have just finished (with a
> great effort) a WWW page including the visualization of pdb files using Chime.
> Until now, the page has worked properly for my students, 
> but now I am trying to publish it
> so that it becomes available for the rest of the world. 
> However, when accessed through Internet everything becomes a
> mess (the pdb files are not visualized-instead, they are automatically
> saved, and there are also many other errors). The plug-in seems to be properly
> installed, since everything is fine when I load the page directly from
> the hard disk.
> Is there anything I am missing that is necessary to publish the page?
> 
> Thank you very much in advance
> 
> Prof. Jesus Sanz
> 

Dear Professor Sanz,

Are the MIME types correctly installed in your server? 
When using a plug in locally (i.e. the files come from the PC),
the browser itself decides which plug-in to use, according to the
file extensions (*.pdb etc). If the files arrive through the net,
the internet server signals what kind of files (MIME types) are sent and 
which plug-in is to be used. So the appropriate MIME types
have to be installed into the server. This can be done easily by the
system administrator of the server. You can read more about the problem 
and how to solve it in the FAQ file of Chime at www.mdli.com.

with regards

Tamas E. Gunda

************************************************************************
   Dr Tamas E. Gunda                   phone: (+36-52) 316666-2479
   Research Group of Antibiotics       fax  : (+36-52) 310936
   L. Kossuth University               e-mail: tamasgunda@tigris.klte.hu
   POBox 36                            http://www.klte.hu/~gundat               
   H-4010 Debrecen
   Hungary
************************************************************************

++++------+------+------+------+------+------+------+------+------+------+
From: "Jesus M. Sanz" <jmsanz@umh.es>
Date: Fri, 03 Jul 1998 12:59:00 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Thanks to all!

Yes, the solution was in the FAQ. Sorry! I am now
beggining to struggle with all these things and did not know
where to look for.

Thanks again

Jesus Sanz

--------------

--------------------------------------------------------------------------
Prof. Jesus M. Sanz				Tel:(34) 966 658 761
Dep. Bioquimica y Biologia Molecular		Fax:(34) 966 658 780
Universidad Miguel Hernandez			E-mail: jmsanz@umh.es
c/ Monovar s/n, Poligono Carrus, ELCHE, 03206-Alicante, SPAIN
       "Asombrarse es la esencia de la vida"   M. C. Escher
--------------------------------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: Matt Challacombe T-12 <mchalla@t12.lanl.gov>
Subject: isosurfaces 
Date: Wed, 8 Jul 1998 11:01:55 -0600 (MDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Hi RasMolers,

I'd very much like to plot isosurfaces and MOs on top of rasmol
structures with the surface data represented on a grid.  
Advice on alternative vis tools that can do this is appreciated.
I know about DX, but I am looking for something LINUX compatible and
less labor intensive.

Cheers, Matt

+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
Matt Challacombe
Los Alamos National Laboratory    http://www.t12.lanl.gov/~mchalla/
Theoretical Division              email: mchalla@t12.lanl.gov
Group T-12, Mail Stop B268        phone:   (505) 665-5905
Los Alamos, New Mexico  87545     fax:     (505) 665-3909
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

X-VMS-To: RASMOL@LISTS.UMASS.EDU
++++------+------+------+------+------+------+------+------+------+------+
From: bhoagland@foma.wsc.mass.edu
Subject: configuring a mac server to present chime
Date: Fri, 10 Jul 1998 07:40:12 -0400
To: RASMOL@dhcp-srv2.oit.umass.edu

i am currently running webstar 3.0 on a mac server and am having difficulty
configuring the MIME types and suffixes to serve chime presentations.  the
settings i have tried that don't work are as follows:

Action	Suffix	Type	Creator	MIME Type

TEXT	.pdb	TEXT	RSML	chemical/x-pdb
BINARY	.spt	RSML	RSML	application/x-spt

i would greatly appreciate any information about this problem.

thanks,

buzz hoagland

        pdb-l@pdb.pdb.bnl.gov
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: RasMac
Date: Sat, 11 Jul 1998 11:23:53 -0400
To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu,
Cc: cwraight@uiuc.edu

This is a reminder about a rather obscure point of RasMol/Chime selection
syntax which might occasion some frustration.

Colin Wraight has called my attention to 4RCR in which the hetero group
ubiquinone-10 is given the group designation U10.  He notes that the
command 'select u10' fails, while e.g. 'select bcl' succeeds for
bacteriochlorophyll. It took me a while to rediscover the solution.

To quote Roger Sayle from the RasMol manual
(http://www.umass.edu/microbio/rasmol/distrib/rasman.htm), under Atom
Expressions, Primitive Expressions:

"A residue name typically consists of up to three alphabetic characters,
which are case insensitive. Hence the primitive expressions SER and ser are
equivalent, identifying all serine residues. Residue names that contain
non-alphabetic characters, such as sulphate groups, may be delimited using
square brackets, i.e. [SO4]."

This is also mentioned under 'Residue Names' in my overview of select commands
(http://www.umass.edu/microbio/rasmol/seleccmd.htm).

So 'select u10' fails, while 'select [u10]' succeeds.

These also fail

select u10:c
select u108:c

while these succeed

select [u10]8
select [u10]8:c
select [u10]:c
select [u10]c

-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Chime "temporarily not available"...?
Date: Sat, 11 Jul 1998 12:41:58 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

All of the Chime download pages have been "temporarily removed" from 
MDLI's website. 
Anyone know what's going on here? I know their site is undergoing a 
makeover, but other downloads (ie, ISIS) are still there. New Chime 
releases underway, maybe :-) ?

Anyone know if there is a mirror site still up with Chime 1.0 available?

regards,
Slaton Lipscomb
C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

++++------+------+------+------+------+------+------+------+------+------+
From: SKG <skg@asis.com>
Subject: Re: Chime "temporarily not available"...?
Date: Sat, 11 Jul 1998 13:53:07 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

At 12:41 PM 7/11/98 -0800, you wrote:
>All of the Chime download pages have been "temporarily removed" from 
>MDLI's website. 
I ran into this too - do a search on their site - there might still be
other ways to the download.

Steven K. Gill

"It is error alone which needs the support of government. Truth can stand
by itself." 
-- Thomas Jefferson, Notes on Virginia 

++++------+------+------+------+------+------+------+------+------+------+
From: Doug Brecknell <brecknel@chemistry.uq.edu.au>
Subject: Re: Chime "temporarily not available"...?
Date: Mon, 13 Jul 1998 10:53:55 +1000
To: rasmol@dhcp-srv2.oit.umass.edu

At 12:41 PM 11-07-98 -0800, you wrote:
>All of the Chime download pages have been "temporarily removed" from 
>MDLI's website. 
>Anyone know what's going on here? I know their site is undergoing a 
>makeover, but other downloads (ie, ISIS) are still there. New Chime 
>releases underway, maybe :-) ?
>
>Anyone know if there is a mirror site still up with Chime 1.0 available?
>
>regards,
>Slaton Lipscomb
>C4: Computers in Chemistry at Cabrillo College
>http://c4.cabrillo.cc.ca.us/
>

I also encountered this problem, but I found that Chime can still be
downloaded from the MDLI UK site

http://www.mdli.co.uk/

Cheers

Doug Brecknell

        pdb-l@pdb.pdb.bnl.gov
        lsprilus@inherit1.weizmann.ac.il, Mark.Gerstein@yale.edu
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Protein Morpher in Chime
Date: Mon, 13 Jul 1998 17:11:40 -0400
To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu,
Cc: dcr@suna.biochem.duke.edu, jsr@suna.biochem.duke.edu, jls@bnl.gov,

Inspired by David and Jane Richardson's Kinemages, I have succeeded in
implementing kinemage-like displays in the Chemscape Chime plugin for
Netscape Communicator (see the Protein Toggler at
http://www.umass.edu/microbio/chime/morpher/index.htm).  However, for
certain large conformational changes, I found I could not see where each
moiety was "going".  A good example is the calcium-induced changes in the
protein recoverin.

Therefore, I implemented a crude "morphing" movie using linear
interpolation, in which the atoms move in equally spaced increments along a
straight line between their positions in the empirical initial and final
configurations.  This helps a great deal in visualizing and understanding
the conformational change, provided one accepts that the interpolated
intermediate configurations are unrealistic and make no attempt to model
the actual conformational change process.  When the two calcium-binding EF
hands are highlighted, and the calcium-binding amino acids shown in red,
and the morph viewed in stereo, one can actually visualize how calcium
induces the conformational change.  A close-up of a single EF hand, showing
the side-chains, is particularly nice.

Mark Gerstein and Werner Krebs at Yale U (http://bioinfo.mbb.yale.edu) have
developed a more sophisticated morphing calculation in which the
interpolated intermediates are "plausible or semi-plausible".  They were
kind enough to share their atomic coordinate data for their morph of
recoverin, which I have also displayed in Chime.

I have also done morphs of influenza hemagglutinin (low pH change) and
CD11b leukocyte integrin, where the change is proposed to account for the
variable affinity of the metal-ion dependent adhesion site (MIDAS) for
ligand, tho these are not yet adequately documented.

Viewing these requires Navigator/Communicator 4.04 or 4.05 and Chime 2.  At
present Chime 2 is available only for Win95/NT4 systems.  If you have
trouble downloading the Chime 2 installer from the US site (www.mdli.com),
try the UK site (http://www.mdli.co.uk/download/chimedown.html). If you
still have trouble, inquire directly of me by email.

The Chime Morpher is at http://www.umass.edu/microbio/chime/morpher/index.htm

Enjoy! -Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: Serving small files with scripts to RasMac
Date: Tue, 14 Jul 1998 19:08:08 +0300
To: rasmol@dhcp-srv2.oit.umass.edu

Something I noticed which may be of interest:

I was trying to serve a small file (alanine) with the script to display
it as sticks:

load pdb inline
wireframe 40
exit
ATOM      1  C           1      -0.134  -0.047  -0.101
ATOM      2  C           1      -1.379   0.806   0.122
ATOM      3  N           1      -0.093  -1.143   0.915
ATOM      4  C           1       1.098   0.814   0.038
ATOM      5  O           1       1.870   0.931  -0.900
ATOM      6  O           1       1.332   1.418   1.131
ATOM      7  H           1      -0.164  -0.479  -1.099
ATOM      8  H           1      -2.267   0.185   0.022
ATOM      9  H           1      -1.409   1.604  -0.617
ATOM     10  H           1      -1.349   1.238   1.120
ATOM     11  H           1      -0.937  -1.734   0.820
ATOM     12  H           1       0.752  -1.722   0.764
ATOM     13  H           1      -0.064  -0.733   1.865
TER   
CONECT    1    2    3    4    7
CONECT    2    1    8    9   10
CONECT    3    1   11   12   13
CONECT    4    1    5    6    0
CONECT    5    4    0    0    0
CONECT    6    4    0    0    0

It work OK on Unix as-is, but RasMac requires some extra space to be
filled in between "exit" and the first "ATOM" line, I guess while it
thinks about it.
Six lines of 80 characters (x's) seem to give it enough time. (This is
not usually a problem for normal pdb files with scripts since all the
HEADER information does the same trick).

Kurt

- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +-972-8-9342614
Weizmann Institute of Science   Fax: +-972-8-9344113
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: Warren Gallagher <wgallagh@uwec.edu>
Subject: Re: configuring a mac server to present chime
Date: Tue, 14 Jul 1998 12:11:40 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

14. June, 1998

Re:
>i am currently running webstar 3.0 on a mac server and am having difficulty
>configuring the MIME types and suffixes to serve chime presentations.  the
>settings i have tried that don't work are as follows:
>
>Action	Suffix	Type	Creator	MIME Type
>
>TEXT	.pdb	TEXT	RSML	chemical/x-pdb
>BINARY	.spt	RSML	RSML	application/x-spt
>
>i would greatly appreciate any information about this problem.
>

We are using WebStar 2.1 on an Apple Workgroup Server and the following
suffix mappings work for us:

BINARY  .pdb   TEXT   *    chemical/x-pdb
BINARY  .spt   TEXT   *    application/x-spt

___________________________________________________________________
 Warren Gallagher
  Associate Professor
  Department of Chemistry
  University of Wisconsin-Eau Claire
  Eau Claire  WI  54702-4004
  E-mail: wgallagh@uwec.edu
  TEL:    (715) 836-5388
  FAX:    (715) 836-4979
___________________________________________________________________

                                         

++++------+------+------+------+------+------+------+------+------+------+
From: Duane Sears <sears@lifesci.ucsb.edu>
Subject: Internet Explorer 4.72.3110.0 supports Chime buttons
Date: Sun, 19 Jul 1998 16:10:32 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Chime users,

Although this may be common knowledge to some of you, I was very surprised
to find that the latest version of Microsoft's Internet Explorer
(4.72.3110.0) now supports the Chime 1.0 buttons on my web pages; in
previous versions the buttons didn't appear.  However, these pages load
rather slowly in the IE browser, and on occassion I  have had to refreshed
a page so that buttons appear in their proper places.  

I also tested IE with  web pages that use my variation on Eric's JavaScript
command box (chimway3.js) for entering and recording RasMol commands for
modifying Chime 1.0 plugin images.  In my hands, the command box didn't
work; that is, commands entered in the box did not get recorded in the
message box and nothing happened to the Chime image.  Interestingly, when
Chime buttons on the same page were pushed, the scripted commands  appeared
in the message box and the image was altered accordingly, indicating that
the message box function is okay with IE.  

I others have had made additional observations on IE's performance, I'd be
interested in learning about it.

Duane
__________________________________________________________
Professor Duane W Sears
Department of Molecular, Cellular and Developmental Biology
University of California
Santa Barbara, CA 93106

Phones:

805-893-3499 (Office)  805-893-4272(Lab)  805-893-4724(FAX)

E-mail:  sears@lifesci.ucsb.edu

Instructional web sites @  

  Immunology --   http://mentor.lscf.ucsb.edu/mcdb133/    
  Biochemistry --  http://mentor.lscf.ucsb.edu/mcdb108a/

++++------+------+------+------+------+------+------+------+------+------+
From: SKG <skg@asis.com>
Subject: Re: Internet Explorer 4.72.3110.0 supports Chime buttons
Date: Sun, 19 Jul 1998 18:48:31 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

At 04:10 PM 7/19/98 -0700, you wrote:
>Dear Chime users,
>
>Although this may be common knowledge to some of you, I was very surprised
>to find that the latest version of Microsoft's Internet Explorer
>(4.72.3110.0) now supports the Chime 1.0 buttons on my web pages; in
>previous versions the buttons didn't appear. 

Thanks for that note - although I personally use netscape exclusively, I
know people that don't & this will be helpful.

Steven K. Gill

"It is error alone which needs the support of government. Truth can stand
by itself." 
-- Thomas Jefferson, Notes on Virginia 

References: <3.0.1.32.19980719161032.007591a4@lifesci.ucsb.edu>
X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id AAA04210
++++------+------+------+------+------+------+------+------+------+------+
From: Rick Lee <rick@sciencemedia.com>
Subject: Re: Internet Explorer 4.72.3110.0 supports Chime buttons
Date: Sun, 19 Jul 1998 21:06:59 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

>Thanks for that note - although I personally use netscape exclusively,
I
>know people that don't & this will be helpful.

Well, the point is not what's a user's preference is, but rather for
people developing the web pages: Is a substantial percentage of the
prospective audience cut out? A developer has no control over the
audience. For me, this is great news that I missed, since I too use
Netscape. 

Duane, is this simply 4.01, or is it the new version released with
Windows 98?

Rick

********************************************
*  Richard H. Lee, PhD
*  Editor/Lead Scientist, Biochemistry
*  rick@sciencemedia.com
*
*  ScienceMedia, Inc.
*  6540 Lusk Blvd., Suite C148
*  San Diego, CA 92121
*
*  TEL: 619/625-9261, Ext. 7
*  FAX: 619/625-9262
*
*  http://www.sciencemedia.com
*********************************************  

References: <3.0.3.32.19980719184831.0068f954@asis.com>
 <3.0.1.32.19980719161032.007591a4@lifesci.ucsb.edu>
X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id UAA06882
++++------+------+------+------+------+------+------+------+------+------+
From: Duane Sears <sears@lifesci.ucsb.edu>
Subject: Re: Internet Explorer 4.72.3110.0 supports Chime buttons
Date: Mon, 20 Jul 1998 17:43:33 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

Rick,

The 4.01 version is downloadable from the MS web site and works with
Windows 95; I haven't installed Windows 98 yet.

Duane

At 09:06 PM 7/19/98 -0700, you wrote:
>>Thanks for that note - although I personally use netscape exclusively,
>I
>>know people that don't & this will be helpful.
>
>Well, the point is not what's a user's preference is, but rather for
>people developing the web pages: Is a substantial percentage of the
>prospective audience cut out? A developer has no control over the
>audience. For me, this is great news that I missed, since I too use
>Netscape. 
>
>Duane, is this simply 4.01, or is it the new version released with
>Windows 98?
>
>Rick
>
>********************************************
>*  Richard H. Lee, PhD
>*  Editor/Lead Scientist, Biochemistry
>*  rick@sciencemedia.com
>*
>*  ScienceMedia, Inc.
>*  6540 Lusk Blvd., Suite C148
>*  San Diego, CA 92121
>*
>*  TEL: 619/625-9261, Ext. 7
>*  FAX: 619/625-9262
>*
>*  http://www.sciencemedia.com
>*********************************************  
>
>
__________________________________________________________
Professor Duane W Sears
Department of Molecular, Cellular and Developmental Biology
University of California
Santa Barbara, CA 93106

Phones:

805-893-3499 (Office)  805-893-4272(Lab)  805-893-4724(FAX)

E-mail:  sears@lifesci.ucsb.edu

Instructional web sites @  

  Immunology --   http://mentor.lscf.ucsb.edu/mcdb133/    
  Biochemistry --  http://mentor.lscf.ucsb.edu/mcdb108a/

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Win98 vs rasmol and Chime
Date: Tue, 21 Jul 1998 09:57:13 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

I've been trying to keep my head in the sand re: Windows 98.  But it seems
to be a reality...

Does anyone have experience with compatibility of:

Win98 with 32-bit RasWin?

Win98 with Chime 1 for Win95?

Win98 with Chime 2 beta 3 for Win95?

-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Brian Beck <beck@Ba.chem.uh.edu>
Subject: Rasmol: Redimensioning Radius Max
Date: Tue, 21 Jul 1998 14:14:28 -0500 (CDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Hello all:

   I've got a question about redefining radii dimensions in
   RasMol.

   Some of my work involves simulation of metalloproteins, the
   metal-ligand bonds of which are often greater than the
   500 RasMol/2.0 A limit. I'd like to recompile Rasmol with
   a 750/3.0 limit but I'm unclear which values/token defs
   I might need to change. A quick grep of the source files
   for 500 seems to indicate that I need to alter command.c,
   molecule.c, and script.c , but of course that may be
   simplistic. A scan of the rasmol-list history file gives
   plenty of responses on how to "set radius" etc, but has
   anyone altered the vdw/covalent radius max values. Once
   I redefine the max, I can then alter abstree.h or use
   "set radius" with "set bondmode and" to get the connections
   I need.

   Thanks,

   -Brian

-- 
==============================================================
| Brian W. Beck     |E-mail Address: beck@uh.edu             |
| Dept. Chemistry   |                                        |
| Univ. of Houston  |URL:                                    |
| 220 Fleming       |http://www.chem.uh.edu/www/pettitt/beck |
| Houston, TX, USA  |VOICE    (713) 743-3264                 |
|       77204-5641  |FAX      (713) 743-2709                 |
==============================================================

References: <0EWG00JK19PMTT@pobox1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: Win98 vs rasmol and Chime
Date: Tue, 21 Jul 1998 21:35:30 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Eric Martz wrote:
> 
> I've been trying to keep my head in the sand re: Windows 98.  But it seems
> to be a reality...
> 
> Does anyone have experience with compatibility of:
> 
> Win98 with 32-bit RasWin?
Works absolutely stable and without any problems over here.

> Win98 with Chime 1 for Win95?
Seems to work, although I haven´t had a deeper look at it.

> Win98 with Chime 2 beta 3 for Win95?
Can´t tell anything about it, as it seems, that there are problems with the
MSI-site.

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

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References: <9807211914.AA28985@Ba.Chem.UH.EDU>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: Rasmol: Redimensioning Radius Max
Date: Tue, 21 Jul 1998 23:00:57 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Brian Beck wrote:
> 
> Hello all:
> 
>    I've got a question about redefining radii dimensions in
>    RasMol.
> 
>    Some of my work involves simulation of metalloproteins, the
>    metal-ligand bonds of which are often greater than the
>    500 RasMol/2.0 A limit. I'd like to recompile Rasmol with
>    a 750/3.0 limit but I'm unclear which values/token defs
>    I might need to change. A quick grep of the source files
>    for 500 seems to indicate that I need to alter command.c,
>    molecule.c, and script.c , but of course that may be
>    simplistic. A scan of the rasmol-list history file gives
>    plenty of responses on how to "set radius" etc, but has
>    anyone altered the vdw/covalent radius max values. Once
>    I redefine the max, I can then alter abstree.h or use
>    "set radius" with "set bondmode and" to get the connections
>    I need.
> 
>    Thanks,
> 
>    -Brian

Hi,

I'm not sure having understood the problem but maybe you canchange these
values in molecule.c:

#define MaxHBondDist   ((Long)300*300)
#define MaxBondDist    ((Long)475*475)
#define MinBondDist    ((Long)100*100)
#define AbsMaxBondDist 600

Allow 'AbsMaxBondDist' and 'MaxBondDist' a larger distance may solve
your problem on the level of code modifications in rasmol.

If you use the 'connect true' command in rasmol the above values are not
used, instead
rasmol decides for bond or not bond by calculating the sum of the
covalent radius of the participating atoms + 1.4 A (look for function
'TestBonded' in molecule.c). So it might be a good idea to have a closer
look at the vdw-radius of the metalls in abstree.h .

	hope to help,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen
Germany
phone: +49-551-399654   | fax  : +49-551-393805
email: amuelle3@gwdg.de | http://www.roko.goe.net/~amuell4/

X-ZSender: rowland.geoff@zetnet.co.uk
++++------+------+------+------+------+------+------+------+------+------+
From: Geoffrey Rowland <rowland.geoff@zetnet.co.uk>
Subject: Compiling Rasmol with MingW32
Date: Wed, 22 Jul 1998 19:34:53 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

Dear all,

Has anyone had any success in compiling Rasmol for Win95(98?)/NT 
using Mingw32 ?

Mingw32 can be freely downloaded as zipped executable files from:

http://agnes.dida.physik.uni-essen.de/~janjaap/mingw32/download.html

For information purposes, I reproduce a short description of Mingw32:

Ming32 is short for the Minimalist GNU-Win32 package which allows the 
use of GCC (the GNU compiler) on Win32 platforms like Windows 95 or 
NT to compile "native programs".  In this case "native means programs 
which don't require extra DLLs like the Cygwin DLL.  Mingw32 programs 
use CRTDLL.DLL to provide their C run time library functions, and 
CRTDLL is supplied with all current Win32 platforms. Thus the 
programs are lightweight, easy to distribute, and do not 
automatically fall under the GNU public licence.

I'm new to C programming/compiling, but by rummaging around the gcc 
and makefile help files, together with the alternative makefiles 
provided with the rasmol source code I have come up with what seems 
to be (to my uneducated eye!) a reasonable makefile - with the 
exception of the last part dealing with raswin.rc and raswin.idm.

In the existing Windows NT makefile (Makefile.nt) the offending lines are:

raswin.res:     raswin.rc raswin.idm
  $(RC) /fo raswin.res /r raswin.rc

Any suggestions how to translate these from (what I presume is) 
Microsoft Visual C into Mingw32/GNU C ?

Many thanks,

Geoff Rowland

References: <1998072219345376239@zetnet.co.uk>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: Compiling Rasmol with MingW32
Date: Wed, 22 Jul 1998 23:40:14 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Geoffrey Rowland wrote:
> 
> Dear all,
> 
> Has anyone had any success in compiling Rasmol for Win95(98?)/NT
> using Mingw32 ?
> 
> Mingw32 can be freely downloaded as zipped executable files from:
> 
> http://agnes.dida.physik.uni-essen.de/~janjaap/mingw32/download.html
> 
> For information purposes, I reproduce a short description of Mingw32:
...

Hi,

Hm, I'm not a windows-programmer, but what about the header files for
the
GUI? RasMol uses MS-C++ specific stuff to create the Windows etc., hm...
maybe I'm wrong and it uses only routines of the MS-classlibraries
included in every win95/NT distribution.
I'm really sceptic about compiling AND linking raswin with a non
MSC++-Compiler, but nevertheless if it's possible it'll be  really
great, so let me know about it ;-) ..., 
but I don't believe that's possible without hacks in the raswin-code!
> 
> I'm new to C programming/compiling, but by rummaging around the gcc
> and makefile help files, together with the alternative makefiles
> provided with the rasmol source code I have come up with what seems
> to be (to my uneducated eye!) a reasonable makefile - with the
> exception of the last part dealing with raswin.rc and raswin.idm.
> 
> In the existing Windows NT makefile (Makefile.nt) the offending lines are:
> 
> raswin.res:     raswin.rc raswin.idm
>   $(RC) /fo raswin.res /r raswin.rc
> 
> Any suggestions how to translate these from (what I presume is)
> Microsoft Visual C into Mingw32/GNU C ?

Sorry, no suggestions. These are files of the description of the GUI for
raswin, maybe these are MSC++-specific, too. 

I don't want to advertise for unix systems but it's much easier to
develope C-programms under unix than under win. Try to compile a
programm for a Borland C-System with a MSC++-Compiler ... . But maybe
rasmol is protable for this purpose, because it's code is really good
structured and most plattform independant as possible (I guess!). 

At all: I'm interested in any experineces and advances to port rasmol to
any kind of free available compiler! So, if the group is not the right
place for this discussion (don't know) and there are others interested
in questions about porting rasmol to free win-c-systems and maybe
improoving rasmol at all let me know, maybe we can discuss this directly
(I don't know how much the group is interested in this).

	sorry to be not able to help (at the moment) - but that's my current
opinion,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen
Germany
phone: +49-551-399654   | fax  : +49-551-393805
email: amuelle3@gwdg.de | http://www.roko.goe.net/~amuell4/

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Compiling Rasmol with MingW32
Date: Wed, 22 Jul 1998 16:52:18 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Regarding Geoffrey Rowland's inquiry about using an unusual C compiler for
RasMol on Windows: In late 1996 I inquired of Roger Sayle which C compiler
I should get if I wished to compile RasMol for Windows.  He replied that if
it mattered which compiler I used, he considered that to be a bug. (I never
got around to trying it.) So, Geoff, seems if you press on you should
succeed. Let us know.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <0EWI00JJYNLFBF@pobox1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: "Francis M.J. Hsieh" <mjhsieh@life.nthu.edu.tw>
Subject: Re: Compiling Rasmol with MingW32
Date: Thu, 23 Jul 1998 09:17:31 +0800
To: rasmol@dhcp-srv2.oit.umass.edu

On Wed, Jul 22, 1998 at 04:52:18PM -0400, Eric Martz wrote:
> Regarding Geoffrey Rowland's inquiry about using an unusual C compiler for
> RasMol on Windows: In late 1996 I inquired of Roger Sayle which C compiler
> I should get if I wished to compile RasMol for Windows.  He replied that if
> it mattered which compiler I used, he considered that to be a bug. (I never
> got around to trying it.) So, Geoff, seems if you press on you should
> succeed. Let us know.

hmmm... MingW32 or djgpp with rxdjnt are clone of gcc on x86 under
windows/dos... If Geoffrey solve the resource file, it can be compile
without problem.
-- 
Francis M. J. Hsieh      | Email:   mjhsieh@life.nthu.edu.tw
Life Science Department, | Webpage: http://www.life.nthu.edu.tw/~mjhsieh/
National Tsing Hua Univ, | Voice:   +886 3 5715131 ext 3482
HsinChu, Taiwan Republic | 	    +886 3 5715649

References: <0EWI00JJYNLFBF@pobox1.oit.umass.edu> <19980723091731.58045@life.nthu.edu.tw>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: Compiling Rasmol with MingW32
Date: Thu, 23 Jul 1998 03:35:24 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Francis M.J. Hsieh wrote:
> 
> On Wed, Jul 22, 1998 at 04:52:18PM -0400, Eric Martz wrote:
> > Regarding Geoffrey Rowland's inquiry about using an unusual C compiler for
> > RasMol on Windows: In late 1996 I inquired of Roger Sayle which C compiler
> > I should get if I wished to compile RasMol for Windows.  He replied that if
> > it mattered which compiler I used, he considered that to be a bug. (I never
> > got around to trying it.) So, Geoff, seems if you press on you should
> > succeed. Let us know.
> 
> hmmm... MingW32 or djgpp with rxdjnt are clone of gcc on x86 under
> windows/dos... If Geoffrey solve the resource file, it can be compile
> without problem.

hmm,  wonderfull ... :-)))


-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen
Germany
phone: +49-551-399654   | fax  : +49-551-393805
email: amuelle3@gwdg.de | http://www.roko.goe.net/~amuell4/

References: <1998072219345376239@zetnet.co.uk> <35B6785D.41344268@gwdg.de>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: Compiling Rasmol with MingW32
Date: Thu, 23 Jul 1998 00:33:10 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Arne Mueller wrote:

> At all: I'm interested in any experineces and advances to port rasmol 
> to any kind of free available compiler! So, if the group is not the 
> right place for this discussion (don't know) and there are others 
> interested in questions about porting rasmol to free win-c-systems and 
> maybe improoving rasmol at all let me know, maybe we can discuss this 
> directly (I don't know how much the group is interested in this).

Well, I´m not really a programmer (and I dont know much about C beside what is
neccessary to compile and tweak some progs a little bit), but I would find it
very interesting to discuss this theme in public in this list.

Shouldn´t be a great problem, as there isn´t much traffic here, so no one
should be upset about some more mails per day.

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

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References: <1998072219345376239@zetnet.co.uk> <35B6785D.41344268@gwdg.de>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Compiling Rasmol with MingW32
Date: Thu, 23 Jul 1998 16:09:37 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Arne and Marc: yes, please continue this discussion on this list as some of
us are very interested in getting RasMol compiled for Windows with free
compilers to permit enhancements to be distributed.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <0EWI00JJYNLFBF@pobox1.oit.umass.edu> <19980723091731.58045@life.nthu.edu.tw> <35B6AF7C.C45E4C9F@gwdg.de>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: Compiling Rasmol with MingW32
Date: Thu, 23 Jul 1998 22:31:00 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Arne Mueller wrote:

> hmm,  wonderfull ... :-)))
Wouldn´t it be a great idea to provide an "official" binary release of 2.6x
for different platforms?

Or is this just meant as an intermediate snapshot until the next version comes
out???

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

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X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by dhcp-srv2.oit.umass.edu id PAA25607
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller  <amuelle3@gwdg.de>
Subject: Re: Compiling Rasmol with MingW32
Date: Fri, 24 Jul 1998 21:14:30 +0200 (MET DST)
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: rasmol@dhcp-srv2.oit.umass.edu

On Thu, 23 Jul 1998, Marc Saric wrote:

> Arne Mueller wrote:
> 
> > hmm,  wonderfull ... :-)))
> Wouldn´t it be a great idea to provide an "official" binary release of 2.6x
> for different platforms?

Hi All,

I think that's the point where I've to be honest ... . Some weeks ago I
released RasMol2.6bx1 in source-code format for unix. I wrote that it
won't be a problem to compile this version under win95 with MS-Visual C++.
Right - it compiled without significant problems. Alas, the program did't
do what it does under unix. First, the commandline under win95 is
different from a native unix-terminal, resulting in a lot of trash comming
on the comandline window under win95. I was able to fixe this problem,
because Roger Sayle wrote the nice functions 'WriteString' and 'WriteChar'
which are terminal independant. So I changed all the 'fprintf' lines of
my code which prints to the terminal to 'WriteString' lines. So the
terminal problem is solved. The second problem is the povray output. I've
to admit that I was really surprised that it doesn't wokr in a right way
under  win. The reason is that the coordinate system RasMol uses under win
it different from that of the unix version. The molecule is not in the
right position when creating a povray file! By now, I was not able to fix
the problem. So there exist a win95 binary of RasMol2.6bx1 but without
working povray support. So I didn't release it.

> 
> Or is this just meant as an intermediate snapshot until the next version comes
> out???

Hm, there are several ideas about enhancing RasMol, small things and huge
projects, but at the moment I've to write my diploma thesis, so there's
not enough time to improove things, sorry. 

There are also two ugly known bugs in RasMol which have to be fixed,
currently I've only a "half solution" for one of it.

1. Zooming a wireframe model to it's maximum and then changeing the
representation to trace or cartoons (a smoothed representation) crashes
rasmol! The overflowing array is known but not changed yet ...

2. On 16, 24 or 32 bit displays under X11 (unix) you might get probelms
saving a raster file (ppm, sun raster, rgb, raster postscript ...). The
colors can be inverted or something like this. This is because different
X-Servers store the bits describing  (r)ed, (g)reen, (b)lue in different
orders. At the moment RasMol uses only one order! I've fixed the probelm
for 24 and 32 bit Displays, but 16 bit is a strange kind of probelm for
me... . Note, you won't have any problems in 8 bit and vector-formats
(Roger said).

At all: RasMol is NOT at it's end (of developement), things have to go 
on! It's not very difficult to understand  (parts) of the RasMol code
for a C-programmer. So, why not spend some time to realize your ideas? 

That's the point where it's important to keep RasMol most platform
independant and to find a way to build it with free compilers so that
everyone who want is able to realize his/her ideas!

	Thanks,

	Arne

> 
> -- 
> 
> Bye,
> 
> Marc Saric

X-ZSender: rowland.geoff@zetnet.co.uk
++++------+------+------+------+------+------+------+------+------+------+
From: Geoffrey Rowland <rowland.geoff@zetnet.co.uk>
Subject: Re: Compiling Rasmol with MingW32
Date: Sat, 25 Jul 1998 03:53:30 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

Hello again

Many thanks for all your encouraging feedback with regard to 
compiling RasMol for windows with mingw32 - although I do appear to 
have bitten off rather more than I can chew!

All I wanted to do was some minor tinkering with the RasMol source 
code followed by a quick recompile to see if it worked.

Firstly, I intended to adjust some of the covalent radii and van der 
Waals radii in abstree.h so that they were more suitable for 
displaying some inorganic structures - the biochemists amongst you 
may not have noticed just how BIG germanium is.

Secondly, I hoped to fix the related problems of how the coordinate 
axes (Set Axes) and unit cell (Set Unit Cell) are drawn. As I 
understand it, the y-axis and b-edge of the unit cell point in the 
wrong direction.  I'm fairly sure a fix would only involve swapping a 
few + signs for - signs in the relevant bits of render.c.

(It has also just occurred to me that this might be related to the 
different coordinate systems in Windows and Unix which Arne has just 
noted - but then again it might not!)

If anyone else wants to do this, I'll be glad to provide a few more 
details.  The same problems were also present in Chime, although may 
be fixed in the Chime2beta3 release (I've not tried this yet).

To get back to the mingw32 compiling.......

I think that adding the windows resources may be solved as I have now 
discovered the windres utility which should do the job.  Part of my 
confusion was that windres works in a different way to the process in 
MS Visual C++.  As far as I now understand it (and PLEASE let me know 
if you know better!) windres can directly compile raswin.rc to an 
object file (which I have called resource.o) and this can then be 
linked with the other object files to make raswin.exe.  In MS Visual 
C++ raswin.rc is converted into an intermediate file type, 
raswin.res, and the compiling is completed as part of the linking process.

However there may be more of a problem in that, although the mingw32 
release has most of the windows libraries and headers that RasMol 
needs, it apparently does not (fully) support Dynamic Data Exchange.  
Specifically the header dde.h (and any other included files?) is 
absent.  The Microsoft version of the dde headers are freely 
available but apparently need a bit of hacking in order to work with 
mingw32.  From trawling the gnuc win32 e-mail archive it seems that 
others have already done this and so I have sent off a few 
speculative requests to see if some kind programmer will come up with 
the goods.

I'll let you know if I make any further progress, although based on 
my experience so far it could be some time.  Just buying MS Visual 
C++ is looking increasingly attractive.  Another notch in Bill Gates' bedpost!

Regards,

Geoff

++++------+------+------+------+------+------+------+------+------+------+
From: nyitray@ludens.elte.hu
Subject: RE: Rasmol: Redimensioning Radius Max
Date: Mon, 27 Jul 1998 13:33:25 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

X-ZSender: rowland.geoff@zetnet.co.uk
++++------+------+------+------+------+------+------+------+------+------+
From: Geoffrey Rowland <rowland.geoff@zetnet.co.uk>
Subject: LCC-Win32: an alternative FREE Win95/NT compiler?
Date: Mon, 27 Jul 1998 23:19:11 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

Dear all - particularly those daft enough to still be interested in 
using free C compilers for RasMol,

As a follow up to my earlier postings on the Mingw32 compiler I would 
also like to draw your attention to yet another FREE C compiler for 
Windows 95/NT, namely LCC-Win32 at:

      http://www.cs.virginia.edu/~lcc-win32/

On the face of it this package seems to be a better bet than Mingw32. 
It is rather user friendly (it has a proper Integrated Development 
Environment) and appears to have all the necessary headers and 
libraries for RasMol (at least in name).  The Makefiles have a 
similar structure to those produced by NMAKE in MS Visual C++ and the 
way the windows resources are handled is also like MS Visual C++.

Even if it dosn't work for RasMol (see below) it looks to be a good 
package for learning or tinkering with C programming without having 
to buy one of the commercial compilers.

I have had a quick go at compiling RasMol for Windows 95 (i.e. 
raswin32.exe) from the source code for version 2.6 beta 2a - but 
without success. As I do not have access to a bona fide compiler I 
have no idea whether the problem(s) are with the RasMol source code, 
the LCC-Win32 compiler, because I am doing something silly, or some 
horrible combination of these. 

It would be really nice if some kind person, who actually can compile 
RasMol for Windows 95/NT (using MS Visual C++ or whatever), would 
also have a go with LCC-Win32 and report their opinion of the package 
(it is simple to download and install).

Many thanks,

            Geoff

++++------+------+------+------+------+------+------+------+------+------+
From: Marc Hansen <mhansen@cse.ucsc.edu>
Subject: Q: any way to send multiple commands?
Date: Mon, 27 Jul 1998 18:30:21 -0700
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: mhansen@cse.ucsc.edu

Hi, I am working on a tool for visualizing alignments
of proteins with unknown structures to proteins with
known structures.  We have an alignment tool which will
color the alignment columns according to criteria such
as residue similarity, and then color the structure
displayed in rasmol with the same colors. If you're
interested, you can read about the project at
http://tito.ucsc.edu/dinamo (we're currently tracking
down a weird checkbox menu bug, so it's not working).
Our problem is that the rasmol display flickers each
time it processes a color command.

Here's my question: Is there a way to send several
commands to rasmol that won't cause this flickering?
I know in Chime you can send commands separated by
a colon, and using tcl/tk, you can enclose multiple
commands in brackets. Using these systems we get no
flickering, but I'd like to be able to do this
directly from the command line.

More info: Our program is written in Java, and we're
writing the commands directly to rasmol.  Until the
java/tk api is finished ('send' isn't implemented 
yet), I'd rather not use tcl/tk becase it would require
us to write java native interface code, which is much
less portable. Plus, it would mean maintaining separate
modules instead of one.

Along those lines, is there any new info on inter-
process communication techniques that are portable
to mac and windows?  I read the old thread on this
in the newsgroup archive, but I think maybe it's
a bit dated by now.  For example, it seems that when
tcl/tk 8.1 is finished, it's 'send' command will work
on the mac and windows platforms too. The beta version
of 8.1 I took a look at on my mac has 'send' supported
only within the same application.  Has anyone tried the
windows version yet?

As for sockets, on the mac you need to have a socket
server (such as a web server) running in order to use
these, right?

I know the mac doesn't directly support the concept
of pipes, but I thought that using Symantec's
Think C, you could add in a unix compatibility library
that would allow you to do things like print to stdout
and read from stdin using a command-line widget that
gets created for you "automatically".  Would it be
possible to use such a library to let another process
write commands to rasmol on the mac? Has anyone tried
anything like this on either the mac or windows?

For now, it seems like one nice thing to do on the
mac side would be to implement the 'do script'
applescript command to allow applications to send
commands to rasmol.  I made a half-hearted attempt
to get this going over the weekend, but wasn't even
able to compile the plain rasmol on my mac due to
a bunch of compiler errors (mostly about old gui
calls?)

Maybe next weekend I'll take a look at writing a
test program on the mac to write to stdout and 
read from stdin if I can find my old Think C
compiler (I'm using CodeWarrior right now).

thanks in advance for any advice,
marc

Marc Hansen
mhansen@cse.ucsc.edu

Computer Graphics Department
University of California, Santa Cruz
Santa Cruz, CA 95064

++++------+------+------+------+------+------+------+------+------+------+
From: "Fernando Gabriel Ranea  " <fgranea@microb.ffyb.uba.ar>
Subject: Microbiological Web Site
Date: Mon, 27 Jul 1998 22:13:12 ARG
To: rasmol@dhcp-srv2.oit.umass.edu

Dear RasMolers:

	I'm Fernando G. Ranea and a weeks ago I have sent a mail related to a
microbiological site that I am building. Well, now I have moved this site to
its owner domain:

	http://www.microbiologia.com.ar

	In this new domain, there are new and improved graphics, new images in
Virtual Reality format (VRML 2.0) and a Tutorial with CHIME images related to
DNA, Beta-lactamics Antimicrobial Agents and the Lipopolissacharide. Moreover,
the section related to Antimicrobial Agentes contains ChemSymphony Java
Applets and it allows rotate the molecules "on line" like Chime Plug-in.
However, actually, this site is only avaidable in spanish but I am working to
translate some section to english.
	There are more molecules for download in the download zone!

Tutorial Insanity: http://www.microbiologia.com.ar/micro3d/tutorial.html

Virtual Insanity: http://www.microbiologia.com.ar/micro3d/virtual.html

	Regards,

Fernando Gabriel Ranea 
fgranea@microb.ffyb.uba.ar

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Another Windows 95/RasMol issue ---- DDE
Date: Tue, 28 Jul 1998 09:45:24 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

This message is from Andrew Coulson (andrewc@srv0.bio.ed.ac.uk; redirected
to the list by Eric Martz for technical reasons).

> It would be really nice if some kind person, who actually can
> compile RasMol for Windows 95/NT (using MS Visual C++ or whatever),
> would also have a go with LCC-Win32 and report their opinion of the
> package (it is simple to download and install).

May I use this as a link to another plea to some kind Windows 95 C
expert? Windows versions of RasMol up to 2.5 included support for DDE.
This was essential to allow other programs to communicate or control
RasMol in MS Windows, and was the basis of Roger Sayle's interface
program RasMenu -- and also of a set of Visual Basic programs which I
was developing to simplify creating animated scripts (and to view the
results). 

These programs didnt work at all with 2.6beta in Windows 95
so I asked Roger what the problem was. I dont remember the full story,
but the gist of it was that at that stage Windows 95 did not support
DDE, and Microsoft seemed to be giving the impression that it never
would. So there was nothing to be done -- I just consigned all the
work I'd done to the bitbucket of history, stuck another needle into
the private parts of the wax doll called Gates which I keep for this
purpose, and thought no more about it. 

However, a few weeks ago Stuart Green 
(S.M.Green@chemistry.leeds.ac.uk) pointed out that Windows 95 now 
does support DDE, and so does tcl/tk, so that, if I've got this 
right, this could form the basis of platform-independent ways of 
other programs communicating with RasMol. To quote Stuart: " .... am 
trying to put together some form of modelling suite using rasmol as 
the renderer. The beauty of tcl/tk is that its portable between Unix 
and Windows. Prior to tcl8.1 you could only communicate with 
X-windows based RasMol using the "send" command. Now, tcl8.1 offers a 
dde communication service - this definitely works with Win95 as I can 
see from wish (tcl/tk windowing shell) other applications that 
support DDE and control them via this mechanism (eg. netscape)....." 

So, is there anyone reading this with the expertise and inclination 
to put back whatever is needed to make DDE work into RasMol 2.6beta? 
The world would be jolly grateful; well, I would be. And Stuart; and 
Bill Gates, of course....

Andrew Coulson

++++------+------+------+------+------+------+------+------+------+------+
From: Marc Hansen <mhansen@cse.ucsc.edu>
Subject: no picking in cartoon mode?
Date: Tue, 28 Jul 1998 14:20:33 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

I'm running the irix version of rasmol 2.6.  I noticed that
I can pick atoms in backbone mode but not in cartoon mode.
Does anyone know how to get picking in cartoon mode?  Or does
anyone know where to tweak the source code to get this working?

thanks,
-marc

Marc Hansen
mhansen@cse.ucsc.edu

Computer Graphics Department
University of California, Santa Cruz
Santa Cruz, CA 95064

References: <199807282120.OAA24487@arapaho.cse.ucsc.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: Re: no picking in cartoon mode?
Date: Wed, 29 Jul 1998 08:36:13 +0300
To: rasmol@dhcp-srv2.oit.umass.edu

> Does anyone know how to get picking in cartoon mode?  Or does
> anyone know where to tweak the source code to get this working?
> 

I tried to get around this once by superimposing the backbone atoms (in
wireframe) onto the cartoon.

select all
cartoon
select *.ca,*.c,*.n
wireframe

It looks a little messy, and I was hoping to be able to make the
wireframe 'invisible', but I couldn't manage to do that.

Kurt
-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +-972-8-9342614
Weizmann Institute of Science   Fax: +-972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

References: <199807282120.OAA24487@arapaho.cse.ucsc.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: no picking in cartoon mode?
Date: Wed, 29 Jul 1998 07:44:59 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Marc Hansen wrote:
> 
> I'm running the irix version of rasmol 2.6.  I noticed that
> I can pick atoms in backbone mode but not in cartoon mode.
> Does anyone know how to get picking in cartoon mode?  Or does
> anyone know where to tweak the source code to get this working?
> 
> thanks,
> -marc
> 
> Marc Hansen
> mhansen@cse.ucsc.edu
> 
> Computer Graphics Department
> University of California, Santa Cruz
> Santa Cruz, CA 95064

Hi,

currently you cannot pick anything in any "smoothed" representation
(ribbons, cartoons, trace). Hacking the source code is a good idea,
beacause, picking in cartoons is offten needed, but I cannot exactly say
where to to apply a hack. Maybe you've to do this in "repres.c" where
RasMol calculates the splines to interpolate between (C-Aplha ?)
atoms - this important, because you've to calculate to which "point"
(atom) the current mouse-clicked point belongs.

	good luck & greetings,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen
Germany
phone: +49-551-399654   | fax  : +49-551-393805
email: amuelle3@gwdg.de | http://www.roko.goe.net/~amuell4/

++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: no picking in cartoon mode?
Date: Wed, 29 Jul 1998 18:33:33 +0000
To: Rasmol Mailinglist <rasmol@dhcp-srv2.oit.umass.edu>

Dear All,

Roger Sayle (is he on the list agian?) sent me an email with the
following 
usefull patch for RasMol (it think it works with all RasMol 2.6
versions) 
to pick atoms in all smoothed representations (e.g. cartoons). I've just 
tested it and it really works well, so you've only to follow Rogers 
instructions:  

Roger Sayle wrote:
> 
> In the function "IdentifyAtom" in "render.c", change the following lines
> 
> >    if( !DisplayMode )
> >    {   if( !UseSlabPlane || (SlabMode != SlabSection) )
> >        {   if( DrawBonds )
> >                ForEachBond
> 
> To become the following.  This allows RasMol to pick on alpha carbons or
> nucleic acid phosphorus atoms in any of the "smooth" representations.
> 
> >    if( !DisplayMode )
> >    {   if( !UseSlabPlane || (SlabMode!=SlabSection) )
> +        {   for( chain=Database->clist; chain; chain=chain->cnext )
> +                for( group=chain->glist; group; group=group->gnext )
> +                {   if( group->flag & DrawKnotFlag )
> +                    {   if( IsProtein(group->refno) )
> +                        {   aptr = FindGroupAtom(group,1);
> +                        } else aptr = FindGroupAtom(group,7);
> +                        if( aptr ) TestAtomProximity(aptr,xpos,ypos);
> +                    }
> +                }
> +
> +            /* Double tolerance for spline knots! */
> +            if( IdentFound ) IdentDist >>= 1;
> +
> >            if( DrawBonds )
> >                ForEachBond
> 
> This will select residues that the user has asked to be displayed in a
> smooth representation and not necessarily those being displayed "smooth"
> by RasMol.  For example, to be displayed RasMol requires two consecutive
> residues in a smooth representation, with no chain break in between and
> the peptide carbonyl oxygen atoms to be present.  However the picking
> should be what is required 98% of the time.
> 
> Roger

	Good luck,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen
Germany
phone: +49-551-399654   | fax  : +49-551-393805
email: amuelle3@gwdg.de | http://www.roko.goe.net/~amuell4/

        jls@bnl.gov
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Chime 2.0 for Macintosh
Date: Wed, 29 Jul 1998 11:44:52 -0400
To: newton <newton@sunchem.chem.uga.edu>
Cc: chrism@mdli.com, FranklinA@mdli.com, rasmol@dhcp-srv2.oit.umass.edu,

Dear Dr. Newton:

You are one of hundreds, probably thousands, anxiously awaiting the release
of Chime 2 for the Macintosh. MDL is quite aware of the demand.  Among
others, Joel Sussman, the Head of the Protein Data Bank has made it clear
to them that he is intensely interested. From what I have been able to
gather, they are working hard on this and there is every reason to believe
it will be released but the date is quite uncertain.  They have had several
involuntary setbacks in personnel on this project but have assigned new
personnel.  It is a large project since Chime 2 has very substantial
enhancements over Chime 1. MDL recently sent me a Mac pre-beta which was
only partially implemented (not really usable yet) but evidence that they
are working on it.

I would have to say that MDL does themselves an unnecessary disservice by
leaving Chime users completely in the dark.  Otherwise, why do you and many
others seek advice from me? I'm sure many are, like yourself, ready to give
up because of the impression that nothing is happening (lack of accurate
and up to date information on MDL's website; lack of announcements to the
380+ subscribers to the RasMol/Chime email list I manage, to the 600-some
subscribers to the PDB email list, and even to their own email list; lack
of feedback to those of us who point out bugs and suggest enhancements). I
am hoping to persuade them to do better in this area. Don't give up!

Please clarify: do you have evidence that Chime 1.0 for the Macintosh fails
to work with a recent Mac OS upgrade?  If so, please give details as I am
unaware of this and don't recall it being mentioned on the RasMol/Chime
email list discussion I manage.

Sincerely, -Eric Martz

At 7/28/98 , you wrote:
>Dear Eric Martz...
>
>Will CHIME ever be updated for Macintosh? I notice that the release date
>keeps moving up by a month or so. This has been happening for over a year
>now.
>
>Please tell me to give up on CHIME 2.0 if no plans exist to issue a new MAC
>version. It appeared to be a wonderful application for use in my courses
>until it failed to work with the recent MAC system upgrade.
>
>Thanks for any encouragement you can realistically offer.
>
>GN
>
>Gary Newton
>Professor, Chemistry
>University of Georgia
>Department of Chemistry
>Athens, GA 30602
>
>(706)-542-1969
>
>email: newton@sunchem.chem.uga.edu
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: 16bit RasWin
Date: Thu, 30 Jul 1998 02:03:56 +0000
To: Rasmol Mailinglist <rasmol@dhcp-srv2.oit.umass.edu>

Dear All,

Does anyone (in this list) use RasWin for windows 3.1 (16 bit NOT
win32)? The thing is that
there's a lot of redundant code in RasMol that could be removed because
it's only necessary for the old 16 bit windows. The probelm I reported
some days ago that POVray-scenes produced with a win95-test version of
Rasmol2.6bx1 are not correct in position (rotation and translation) may
be caused by some parts of this code. In short words: future
developement of RasMol can be more easy when skipping all the old 16bit
windows code! Everytime a developer applies some changes to the graphics
sytem you+ve to think about all these 16 bit specials, and this doesn't
make things easier... . 

So, please send me an email or post to the list if you'll have to use 16
bit RasWin in future (maybe for teaching at school?). Otherwise I'll
kill all the "#INVERT" and some other old windows code in any
developement-versions of RasdMol2.6bx1 (only in case that I'm able to
release RasMol2.6bx1 for windows some day ;-) ... ). 

	Thanks alot and greetings,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen
Germany
phone: +49-551-399654   | fax  : +49-551-393805
email: amuelle3@gwdg.de | http://www.roko.goe.net/~amuell4/

References: <0EWV00685819QB@rfd1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: shoba <shoba@angis.usyd.edu.au>
Subject: Re: Chime 2.0 for Macintosh
Date: Fri, 31 Jul 1998 10:07:52 +1000
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Chimers,

While on the subject,  it would be nice to have Chime for other UNIX
platforms as well, since LINUX and Solaris are quite popular.

Perhaps Chime could be distributed as a platform-independent binary +
a platform-dependent code that can be locally compiled?

Shoba
=======================================================================
Shoba Ranganathan, Ph D                             Tel:+61-2-9351-1860
ANGIS, Bay 16, Suite 104                        Toll free:1-800-728-028
Australian Technology Park                          Fax:+61-2-9351-5694
Eveleigh NSW 1430
Australia                 Personal URL: http://seal.angis.org.au/~shoba
================MolMod Home Page: http://molmod.angis.org.au===========

References: <0EWV00685819QB@rfd1.oit.umass.edu> <35C10AD8.DC8F7C68@angis.org.au>
++++------+------+------+------+------+------+------+------+------+------+
From: "Francis M.J. Hsieh" <mjhsieh@life.nthu.edu.tw>
Subject: Re: Chime 2.0 for Macintosh
Date: Fri, 31 Jul 1998 09:20:40 +0800
To: rasmol@dhcp-srv2.oit.umass.edu

On Fri, Jul 31, 1998 at 10:07:52AM +1000, shoba wrote:
> While on the subject,  it would be nice to have Chime for other UNIX
> platforms as well, since LINUX and Solaris are quite popular.
> 
> Perhaps Chime could be distributed as a platform-independent binary +
> a platform-dependent code that can be locally compiled?

Yes, there are similar demand on unix version Chime. Maybe MDLI should
consider about releasing linux binary of chime plugin :-)

ps. Though we are using BSD as our common platform, I suggest to release
    linux first because there is no plugin support in bsd version netscape
-- 
Francis M. J. Hsieh      | Email:   mjhsieh@life.nthu.edu.tw
Life Science Department, | Webpage: http://www.life.nthu.edu.tw/~mjhsieh/
National Tsing Hua Univ, | Voice:   +886 3 5715131 ext 3482
HsinChu, Taiwan Republic | 	    +886 3 5715649

++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: RasWin/Chime questions
Date: Fri, 31 Jul 1998 21:58:09 +0300
To: RasMol list <rasmol@dhcp-srv2.oit.umass.edu>

The PDB serves files for Chime as chemical/x-pdb mime type, and for
RasMol as application/x-rasmol, allowing both to be configured on Mac
and SGI.
Is it possible to configure Win95 browsers to differentiate the two? (I
get chime opening 'application/x-rasmol' served files unless I disable
it by moving it out of the Plugins folder).

Is it possible to get RasWin to read PDB files _containing_ scripts,
either locally or served as application/x-rasmol, as it is with Mac and
Unix?

For example, from the page: 
http://www.pdb.bnl.gov/pdb-bin/opdbshort?id=1ACJ&fras=1
(or the equivalent from your local PDB mirror)

using the links 1ACJ.Abola_1995.1 or 1ACJ.Abola_1995.2

is it possible get the scripted representation with RasWin?

Kurt
-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +-972-8-9342614
Weizmann Institute of Science   Fax: +-972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: Clifford Felder <cffelder@weizmann.weizmann.ac.il>
Subject: Chemscape Chime 2 is also needed on all popular UNIX Platforms
Date: Wed, 05 Aug 1998 17:58:50 +0300
To: rasmol@dhcp-srv2.oit.umass.edu

I concur with Shoba Ranganathan and Francis M. J. Hsieh, that it is
extremely
important that versions of Netscape/Internet Browser plugin Chemscape
Chime
Versions be made available for all the popular Unix platforms: SGI/Irix,
Dec-Alpha/OSF/ULTRIX, IBM Risc/AIX, HP/HPIX, Sun and LINUX. Maybe a
generic
Unix version could be provided, or a source code that could be compiled
on any
standard C compiler. This is important, because many potential users of
the PDB
and related databases use UNIX-based systems primarily.
  As many such users lack system privilege, it is important that this
plugin,
like the present SGI Chime Version 1, must be able to work from a user's
$HOME/.netscape/plugins folder.
  Thank you very much for your cooperation in this important matter. 
Sincerely, Clifford Felder <cffelder@weizmann.weizmann.ac.il>

References: <35C8732A.41C6@weizmann.weizmann.ac.il>
++++------+------+------+------+------+------+------+------+------+------+
From: Mary Beth Jipping <mbj@venus.chem.stevens-tech.edu>
Subject: Re: Chemscape Chime 2 needed on UNIX Platforms
Date: Wed, 05 Aug 1998 11:50:31 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

My experience that Rasmol isn't available for IRIX either.  I develop
pages on an Octane and find that I can't use Rasmol or Chime in these
pages unless I move to a PC to finish the page.

I can't even preview my proteins at the PDB with Rasmol or Chime.

I agree - Rasmol and Chime are needed for Unix.

MBJipping

References: <35C8732A.41C6@weizmann.weizmann.ac.il> <35C8A977.41C6@venus.chem.stevens-tech.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: Re: Chemscape Chime 2 needed on UNIX Platforms
Date: Wed, 05 Aug 1998 17:42:07 +0300
To: rasmol@dhcp-srv2.oit.umass.edu

> My experience that Rasmol isn't available for IRIX either.  I develop
> pages on an Octane and find that I can't use Rasmol or Chime in these
> pages unless I move to a PC to finish the page.
> 
> I can't even preview my proteins at the PDB with Rasmol or Chime.

Can you explain the problem/operating system version etc. in a bit more
details.
I've used RasMol and Chime successfully with a few different IRIX
versions, on different machines, including an Octane.

Kurt

-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +-972-8-9342614
Weizmann Institute of Science   Fax: +-972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

References: <35C8732A.41C6@weizmann.weizmann.ac.il> <35C8A977.41C6@venus.chem.stevens-tech.edu> <35C86F3F.56A5A499@inn-prot.weizmann.ac.il>
++++------+------+------+------+------+------+------+------+------+------+
From: Mary Beth Jipping <mbj@venus.chem.stevens-tech.edu>
Subject: Re: Chemscape Chime 2 needed on UNIX Platforms
Date: Wed, 05 Aug 1998 12:17:55 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

> > My experience that Rasmol isn't available for IRIX either.  I develop
> > pages on an Octane and find that I can't use Rasmol or Chime in these
> > pages unless I move to a PC to finish the page.
> >
> > I can't even preview my proteins at the PDB with Rasmol or Chime.
> 
> Can you explain the problem/operating system version etc. in a bit more
> details.
> I've used RasMol and Chime successfully with a few different IRIX
> versions, on different machines, including an Octane.
Where do I get the source code?  I don't have a compiler but can compile
on a different machine and bring it over.
Thanks, for answering so fast - don't all answer at once!!!:-)
MBJipping

References: <35C8732A.41C6@weizmann.weizmann.ac.il> <35C8A977.41C6@venus.chem.stevens-tech.edu> <35C86F3F.56A5A499@inn-prot.weizmann.ac.il> <35C8AFE3.446B@venus.chem.stevens-tech.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: Re: Chemscape Chime 2 needed on UNIX Platforms
Date: Wed, 05 Aug 1998 17:57:27 +0300
To: rasmol@dhcp-srv2.oit.umass.edu

> Where do I get the source code?  I don't have a compiler but can compile
> on a different machine and bring it over.

ftp://pdb.pdb.bnl.gov/pub/xternal_software/Rasmol/v2.6beta/RasMol26.tar.gz

For Chime 0.9 on SGI recent versions of IRIX, you may have to start up
Netscape as 
netscape -pseudocolor

Kurt
-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +-972-8-9342614
Weizmann Institute of Science   Fax: +-972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

X-MSMail-Priority: Normal
++++------+------+------+------+------+------+------+------+------+------+
From: "Forrest Shirkey" <fshirkey@ucsd.edu>
Subject: Rasmol Lists
Date: Wed, 5 Aug 1998 09:34:44 -0700
To: <rasmol@dhcp-srv2.oit.umass.edu>

Could One person, please send a mail to this list describing how to
UNSUBSCRIBE.

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: SAVE THIS MESSAGE (RasMol email list unsubscribe info)
Date: Wed, 05 Aug 1998 11:52:14 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

To unsubscribe from the RasMol email list (and for all other information on
administrative matters for the list) please consult
http://www.umass.edu/microbio/rasmol/raslist.htm

This can be found by going to the RasMol Home Page and clicking on Index,
Email discussion.

-Eric Martz (list manager)
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Julia Yu <juliay@mdli.com>
Subject: Re: Chemscape Chime 2 is also needed on all popular UNIX Platforms
Date: Wed, 5 Aug 1998 15:50:44 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

<html>
Hi,<br>
<br>
Chime 0.9z for SGI is available for download at
<a href=3D"http://www.mdli.com/download/acceptsgi.html">http://www.mdli.com/=
download/acceptsgi.html</a>.&nbsp;
However, we are no longer supporting Chime for the SGI/Irix platform, nor
do we plan to support Chime on any other Unix platform.&nbsp; <br>
<br>
Regards,<br>
Julia Yu<br>
Chemscape QA<br>
MDL Information Systems, Inc.<br>
<br>
<br>
At 07:58 AM 8/5/98 -0700, you wrote:<br>
&gt;I concur with Shoba Ranganathan and Francis M. J. Hsieh, that it
is<br>
&gt;extremely<br>
&gt;important that versions of Netscape/Internet Browser plugin
Chemscape<br>
&gt;Chime<br>
&gt;Versions be made available for all the popular Unix platforms:
SGI/Irix,<br>
&gt;Dec-Alpha/OSF/ULTRIX, IBM Risc/AIX, HP/HPIX, Sun and LINUX. Maybe
a<br>
&gt;generic<br>
&gt;Unix version could be provided, or a source code that could be
compiled<br>
&gt;on any<br>
&gt;standard C compiler. This is important, because many potential users
of<br>
&gt;the PDB<br>
&gt;and related databases use UNIX-based systems primarily.<br>
&gt;=A0 As many such users lack system privilege, it is important that
this<br>
&gt;plugin,<br>
&gt;like the present SGI Chime Version 1, must be able to work from a
user's<br>
&gt;$HOME/.netscape/plugins folder.<br>
&gt;=A0 Thank you very much for your cooperation in this important matter.
<br>
&gt;Sincerely, Clifford Felder
&lt;cffelder@weizmann.weizmann.ac.il&gt;<br>
&gt;=20
<BR>
</html>

X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id SAA26627
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Chime 2 documentation gaps: set connect save, initscript
Date: Wed, 05 Aug 1998 17:52:42 -0400
To: rasmol@dhcp-srv2.oit.umass.edu, jch@mdli.com

The following question from Evan P Kransdorf and answer from Tim Maffett
reveal
two important features of Chime 2 which are not documented at MDL's site or my
site. Thanks to Tim for pointing this out to me. See below for more on
undocumented Chime2 features.

>Desciption=I need to connect some heteroatoms in a PDB file with the
>CONECT command.  CHIME does not seem to accept/realize the CONECT tag and
>leaves the heteroatoms unconnected.  I have illustrated this problem on the
>page:
>
>  The problem you are seeing is that
>Chime (and rasmol would do the same) sees that the file has too few
>connect records to have all actual bonds, so all existing CONECT records
>are thrown out and new ones computed from atom-atom distances.
>  Chime 2.0 has a new command, "set connect save", which will tell 
>chime to SAVE all the existing CONEC records *and* compute new connections
>via the normal method.
>  You can tell chime to do this on your example page by adding the
>embed tag:
>
>initscript="set connect save"
>
>  The 'initscript' embed tag allows you to specify a script for chime
>to execute BEFORE it loads the src="" molecule.

Some other commands not yet documented at MDL's site are:

The move and delay commands which are explained at
<http://www.umass.edu/microbio/chime/manual/chimeman.htm>http://www.umass.e
du/microbio/chime/manual/chimeman.htm

and these:

>
> center xyz 2664 3120 545
> translate center center
> set zoom center true
>
> center xyz 2664 3120 545:
> My guess: places the center using rasmol units.
>
> translate center center
> My guess: moves the center to the center of the screen.
>
> set zoom center true
> This one I know: when zooming, the center is held in the center of the
> screen.

-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: CONECT default in Chime 2?
Date: Wed, 05 Aug 1998 18:10:58 -0400
To: rasmol@dhcp-srv2.oit.umass.edu, tim@mind.net

Tim Maffett has raised the question of what the default setting should be
in Chime 2 regarding 'set connect save'.  At present, RasMol and Chime
ignore CONECT records if they are fewer in number than the number of atoms,
except for any CONECT records which specify double or triple bonds.  The
'set connect save' command forces Chime 2 to draw bonds where CONECT
records specify, and in addition to draw bonds where Chime determines they
exist based on distances between atoms.  This allows one or a few CONECT
records to specify bonds which Chime may otherwise fail to show, such as
between metals and other atoms.

My feeling is that 'set connect save' should be the new default since one
can assume that if any CONECT records are present in the PDB file, they
should be shown.  In this case a command would be provided (or may already
exist) such as 'set connect off' to go back to the old mode. Does anyone
have a reason why the default should remain as it is now?

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <35C8732A.41C6@weizmann.weizmann.ac.il> <35C8A977.41C6@venus.chem.stevens-tech.edu> <35C86F3F.56A5A499@inn-prot.weizmann.ac.il> <35C8AFE3.446B@venus.chem.stevens-tech.edu> <35C872D7.106D1C99@inn-prot.weizmann.ac.il>
++++------+------+------+------+------+------+------+------+------+------+
From: shoba <shoba@angis.usyd.edu.au>
Subject: Re: Chemscape Chime 2 needed on UNIX Platforms
Date: Thu, 06 Aug 1998 13:09:27 +1000
To: rasmol@dhcp-srv2.oit.umass.edu

I would like to add start netscape as:
> netscape -visual pseudocolor

I would like to add that Chime 0.9 for SGIs works really well and I have
adatped tutorials and viewers to use Chime.

Works very well with PDB and SCOP Chime scripts as well

Shoba

Kurt Giles wrote:
> 
> > Where do I get the source code?  I don't have a compiler but can compile
> > on a different machine and bring it over.
> 
> ftp://pdb.pdb.bnl.gov/pub/xternal_software/Rasmol/v2.6beta/RasMol26.tar.gz
> 
> For Chime 0.9 on SGI recent versions of IRIX, you may have to start up
> Netscape as
> netscape -pseudocolor
> 
> Kurt
> --
> ---------------------------------------------------------------
> Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il
> Israeli National Node
> Biological Computing Unit       Tel: +-972-8-9342614
> Weizmann Institute of Science   Fax: +-972-8-9466269
> Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
> ---------------------------------------------------------------

-- 
=======================================================================
Shoba Ranganathan, Ph D                             Tel:+61-2-9351-1860
ANGIS, Bay 16, Suite 104                        Toll free:1-800-728-028
Australian Technology Park                          Fax:+61-2-9351-5694
Eveleigh NSW 1430
Australia                 Personal URL: http://seal.angis.org.au/~shoba
================MolMod Home Page: http://molmod.angis.org.au===========

References: <01J090EW82JG9143UP@mdli.com>
++++------+------+------+------+------+------+------+------+------+------+
From: shoba <shoba@angis.usyd.edu.au>
Subject: Re: Chemscape Chime 2 is also needed on all popular UNIX Platforms
Date: Thu, 06 Aug 1998 13:13:43 +1000
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Chimeusers,

It seems MDL has no interest any more in Chime for UNIX users!
Perhaps they could collaborate with someone who can generate the
plug-ins for UNIX platforms?

We can emulate x-terms for UNIX boxes on PC/MACs but not the other way
around!

Shoba

Julia Yu wrote:
> 
> Hi,
> 
> Chime 0.9z for SGI is available for download at
> http://www.mdli.com/download/acceptsgi.html.  However, we are no
> longer supporting Chime for the SGI/Irix platform, nor do we plan to
> support Chime on any other Unix platform.
> 
> Regards,
> Julia Yu
> Chemscape QA
> MDL Information Systems, Inc.
> 

-- 
=======================================================================
Shoba Ranganathan, Ph D                             Tel:+61-2-9351-1860
ANGIS, Bay 16, Suite 104                        Toll free:1-800-728-028
Australian Technology Park                          Fax:+61-2-9351-5694
Eveleigh NSW 1430
Australia                 Personal URL: http://seal.angis.org.au/~shoba
================MolMod Home Page: http://molmod.angis.org.au===========

++++------+------+------+------+------+------+------+------+------+------+
From: Albion Baucom <baucom@gorby.ucsc.edu>
Subject: Loading MDL MOL files with Chime
Date: Thu, 6 Aug 1998 01:00:40 -0700 (PDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Does anyone have any experience with loading MDL mol files using a script?
I am trying to load a new model in an embeded Chime model of type
chemical/x-mdl-molfile using the command

zap; load guanine.mol

or

zap; load mdl guanine.mol

and I am getting back the message 

Requesting guanine.mol ...

but the model never loads. Does anyone know what is going on here? I CAN
load PDB files using the load command ... but mol files dont not work
using this syntax. What is interesting is that I can use the Save As ...
option in the Chime menu and actually save the coordinates! I have tried
changing the display style both in the Chime menu and through a command
line interpreter to insure that it is not a "hidden" model (all display
attributes turned off).

TIA

Albion

Albion E. Baucom
baucom@gorby.ucsc.edu
'79 R65, '71 R75/5 
ABC #2768

UC Santa Cruz
241B Sinsheimer Labs
Santa Cruz, CA 95064
(408) 459-5128

References: <01J090EW82JG9143UP@mdli.com>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: Chemscape Chime 2 is also needed on all popular UNIX Platforms
Date: Thu, 06 Aug 1998 20:38:25 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Julia Yu wrote:
> 
> Hi,
> 
> Chime 0.9z for SGI is available for download at
> http://www.mdli.com/download/acceptsgi.html.  However, we are no 
> longer supporting Chime for the SGI/Irix platform, nor do we plan to 
> support Chime on any other Unix platform.
Isn´t that very short-sighted?? Supporting the one and only monopoly of
Microsoft and a small and proprietary system (Apple) while leaving out the
(especially in the science market) growing Unix (and Linux) part??

Or is it so much more work to port the program to one other platform???

Rasmol can be ported without great problems, so where´s the trouble with
Chime??

It would make this tool much more valuable.

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

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++++------+------+------+------+------+------+------+------+------+------+
From: "Francis M.J. Hsieh" <mjhsieh@life.nthu.edu.tw>
Subject: Example: RasMol as UNIX mozilla plugins
Date: Sun, 9 Aug 1998 15:54:24 +0800
To: rasmol@dhcp-srv2.oit.umass.edu

Hi folks,

I had tried to put rasmol as a netscape plugin using Xswallow (a generic
plugin). It works fine in my FreeBSD machines with my netscape 4.05pr1
though there is a little problem here. (about windows resizing)

Here is the procedure (using my FreeBSD as an example):

fetch the file XswallowSource-1.0.11.tar.gz
Please use archie to find it. (I recommend to use the www service
at http://ftpsearch.ntnu.no/ )

$ gzip -cd XswallowSource-1.0.11.tar.gz | tar xvf -
$ cd PluginSDK30b5/xswallow
$ cp makefile.linux Makefile

Append  -I/usr/X11R6/include string after the CFLAGS line
       ^^^^^^^^^^^^^^^^^^^^^
$ gmake
$ cp xswallow.so ~/.netscape/plugins
  (if you don't have plugins directory, mkdir ~/.netscape/plugins)
$ cp xswallow.conf ~/.netscape

Edit ~/.netscape/xswallow.conf
Add following line into xswallow.conf after the line "# MIME type ...."
chemical/x-pdb; pdb, xyz, ent; /usr/X11R6/bin/rasmol %s ; RasMol ; Embedded PDB
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Restart your Netscape, take it a try.

if your http server support "chemical/x-pdb" mime type it should work.

Of course it needs a lot of works, but this is a quick hack to view
pdb in your unix Netscape window.

-- 
Francis M. J. Hsieh      | Email:   mjhsieh@life.nthu.edu.tw
Life Science Department, | Webpage: http://www.life.nthu.edu.tw/~mjhsieh/
National Tsing Hua Univ, | Voice:   +886 3 5715131 ext 3482
HsinChu, Taiwan Republic | 	    +886 3 5715649

++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: RasMol/Chime predefined sets
Date: Sun, 09 Aug 1998 18:52:16 +0300
To: RasMol list <rasmol@dhcp-srv2.oit.umass.edu>

I've made a Venn diagram trying to relate all pre-defined terms (lower
case) to amino acid, nucleotide and heteroatom names (bold capitals) in
RasMol/Chime:

http://inn-prot.weizmann.ac.il/download/venn.GIF

It contains all but the following terms: BURIED, SURFACE, LARGE, MEDIUM

If you notice anything that's wrong, or want the original Mac files
(where all names and ovals are individual objects) to try and include
the other terms, then please contact me.

Kurt
-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +-972-8-9342614
Weizmann Institute of Science   Fax: +-972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

References: <35CDC5B0.D7F0B2BC@inn-prot.weizmann.ac.il>
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <amuelle3@gwdg.de>
Subject: Re: RasMol/Chime predefined sets
Date: Sun, 09 Aug 1998 18:51:45 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Kurt Giles wrote:
> 
> I've made a Venn diagram trying to relate all pre-defined terms (lower
> case) to amino acid, nucleotide and heteroatom names (bold capitals) in
> RasMol/Chime:
> 
> http://inn-prot.weizmann.ac.il/download/venn.GIF
> 
> It contains all but the following terms: BURIED, SURFACE, LARGE, MEDIUM
> 
> If you notice anything that's wrong, or want the original Mac files
> (where all names and ovals are individual objects) to try and include
> the other terms, then please contact me.
> 

Thanks for that usefull information (I'll pin it next to my computer
...). 

There's also a very usefull site at the embl, which introduces into
chemical properties of aminoacids, it also takes care of the
buried/exposed parameter.

http://www.sander.embl-heidelberg.de/future/aainfo/

	Greetings,

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen
Germany
phone: +49-551-399654   | fax  : +49-551-393805
email: amuelle3@gwdg.de | http://www.roko.goe.net/~amuell4/

++++------+------+------+------+------+------+------+------+------+------+
From: newton <newton@sunchem.chem.uga.edu>
Subject: rasmol with fractional coordinates?
Date: Mon, 10 Aug 1998 07:21:25 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

I am interested in using X-ray unitless fractional coordinates (instead of
orthogonal Angstron coordinates) as direct input to rasmol. Do any of you
know whether this operation is possible?

If the above is possible, can symmetry-related molecules be generated from
the fractional coordinate input?

Thanx,
Gary Newton
newton@sunchem.chem.uga.edu

Gary Newton
Professor, Chemistry
University of Georgia
Department of Chemistry
Athens, GA 30602

(706)-542-1969

email: newton@sunchem.chem.uga.edu

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Venn diagram of predefined sets
Date: Mon, 10 Aug 1998 18:08:06 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Kurt Giles' Venn diagram of the predefined sets is an excellent overview of
these terms for selection in RasMol and Chime.  With his permission, I have
incorporated it into the documents

Select Commands in Chime and RasMol 

http://www.umass.edu/microbio/rasmol/seleccmd.htm

and the

RasMol [Reference] Manual

http://www.umass.edu/microbio/rasmol/distrib/rasman.htm

-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Netscape 4.05 javascript bug
Date: Tue, 11 Aug 1998 11:35:12 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

It appears to me that a bug was introduced into Netscape 4.05 which causes
functions defined in .js javascript files (included in an html file with
<script src="xxx.js"></script>) to become undefined when the html file is
reloaded, or returned to via Back or Forward.  The problem arises ONLY when
the files are viewed from the LOCAL HARD DISK; it does not occur when
viewed from an http server.  I have done all my tests in Windows 95 so I
cannot speak for other platforms. The bug is not present in Navigator 4.04.
Thus, for example, local copies of my noncovalent bond finder or morpher
cannot be used in Nav4.05 but can in Nav4.04.

An example, simplified as much as possible to demonstrate the bug, is at

http://www.umass.edu/microbio/n405/n405.htm

To see the bug, you have to use File, Save As to save the htm file to your
hard disk, and then create file n405.js in the same folder with a text
editor.  It contains these 3 lines:

function defined_in_js_file()
{
        var2 = "<p>Line 2: Function defined in .js file has changed var2.";
}

Then use File, Open page to open n405.htm.

I have reported this to Netscape. I will appreciate enlightening comments
anyone can offer.
-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: SKG <skg@asis.com>
Subject: Re: Netscape 4.05 javascript bug
Date: Tue, 11 Aug 1998 10:06:14 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

At 11:35 AM 8/11/98 -0400, you wrote:
>It appears to me that a bug was introduced into Netscape 4.05

Hi Dr. Martz - I tried your demo page, went to the doc2.htm & pressed the
back button, & 
it worked normally - what am I supposed to see to demo the problem?
I'll try the download trick - meanwhile, I'll reinstall Ntscp 4.04!   Thank
you kindly for your vigilance...........

Steven K. Gill

"It is error alone which needs the support of government. Truth can stand
by itself." 
-- Thomas Jefferson, Notes on Virginia 

++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: RasMol/Chime Venn
Date: Thu, 13 Aug 1998 13:23:01 +0300
To: RasMol list <rasmol@dhcp-srv2.oit.umass.edu>

Will McClure pointed out a mistake in the Venn diagram, which I have now
rectified

RasMol defines TYR as AROMATIC, CYCLIC, HYDROPHOBIC, NEUTRAL  not 
AROMATIC, CYCLIC, POLAR, NEUTRAL as I had.

http://inn-prot.weizmann.ac.il/download/venn.GIF

References: <35D2BE85.D315E32@inn-prot.weizmann.ac.il>
++++------+------+------+------+------+------+------+------+------+------+
From: William R Mcclure <wm0p+@andrew.cmu.edu>
Subject: Quick Reference Card (PDF)
Date: Thu, 13 Aug 1998 08:17:20 -0400 (EDT)
To: rasmol@dhcp-srv2.oit.umass.edu

 The RasMol Quick Reference Card (PDF) has been revised to include the
default mouse bindings for bothWindows and (now also) Mac.
 (Some other tiny changes/additions were also made including URLs for
the RasMol Home Page and the Frames Manual.) It can be copied at:
http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/NAVNOTE.HTM
(link at the bottom of the page).

-Will McClure 

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: RasMol/Chime Venn
Date: Fri, 14 Aug 1998 12:31:27 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

At 8/13/98, you wrote:
>Will McClure pointed out a mistake in the Venn diagram, which I have now
>rectified
>
>RasMol defines TYR as AROMATIC, CYCLIC, HYDROPHOBIC, NEUTRAL  not 
>AROMATIC, CYCLIC, POLAR, NEUTRAL as I had.
>
>http://inn-prot.weizmann.ac.il/download/venn.GIF
> 

Hmmm.  My tests indicate that both RasMol and Chime consider Tyr to be
POLAR and not HYDROPHOBIC.  Here are the tests I did (after opening any
protein containing some tyr):

select tyr

  gives the same atom count as

select tyr and polar

  while

select tyr and hydrophobic

  selects no atoms.

Therefore I believe the original venn diagram was correct!

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <0EXO00BT7WV8BI@rfd1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: Re: RasMol/Chime Venn
Date: Sun, 16 Aug 1998 09:43:42 +0300
To: rasmol@dhcp-srv2.oit.umass.edu

Eric Martz wrote:
> Hmmm.  My tests indicate that both RasMol and Chime consider Tyr to be
> POLAR and not HYDROPHOBIC.

Yes, you're right.
At least it's made me tidy the picture up a bit - now all the groups are
ovals.

New (neater) version at http://inn-prot.weizmann.ac.il/download/venn.GIF

Kurt

-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +-972-8-9342614
Weizmann Institute of Science   Fax: +-972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

X-ZSender: rowland.geoff@zetnet.co.uk
++++------+------+------+------+------+------+------+------+------+------+
From: Geoffrey Rowland <rowland.geoff@zetnet.co.uk>
Subject: rasmol with fractional coordinates?
Date: Sun, 16 Aug 1998 20:18:34 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

The message <l03130300b1f486c2797f@[207.43.201.33]>
  from  newton <newton@sunchem.chem.uga.edu> contains these words: 

> I am interested in using X-ray unitless fractional coordinates (instead of
> orthogonal Angstrom coordinates) as direct input to rasmol. Do any of you
> know whether this operation is possible?

> If the above is possible, can symmetry-related molecules be generated from
> the fractional coordinate input?

> (snip)

You can use the program Babel to interconvert many different 
molecular modelling file formats.
Although I am not familiar with all of these you can certainly 
convert CDS CSSR (.xr) files, which use fractional coordinates, to 
Brookhaven PDB (.pdb) files which use orthogonal coordinates and can 
be read by RasMol/Chime.

Babel is available for Unix and Dos from:

          http://mercury.aichem.arizona.edu/babel.html

If you use Windows you can also download a useful graphical 
interface, BabelWin.

There is also a web-based interface for Babel at:

          http://orville.ucsc.edu/cgi-bin/ferinczbin/convert

Although Babel converts the atomic coordinates you will have to use a 
text editor to add the crystallographic information. For .pdb files 
this is contained in the CRYST1 line which has the following format 
(edited from PDB documentation):

COLUMNS       DATA TYPE      FIELD         DEFINITION
-------------------------------------------------------------
 1 -  6       Record name    "CRYST1"
 7 - 15       Real(9.3)      a             a (Angstroms).
16 - 24       Real(9.3)      b             b (Angstroms).
25 - 33       Real(9.3)      c             c (Angstroms).
34 - 40       Real(7.2)      alpha         alpha (degrees).
41 - 47       Real(7.2)      beta          beta (degrees).
48 - 54       Real(7.2)      gamma         gamma (degrees).
56 - 66       LString        sGroup        Space group.
67 - 70       Integer        z             Z value (number of 
polymeric chains in a unit cell).

Examples
         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
CRYST1   52.000   58.600   61.900  90.00  90.00  90.00 P 21 21 21    8

CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1

CRYST1   42.544   69.085   50.950  90.00  95.55  90.00 P 1 21 1      2

The CRYST1 line should be inserted before the ATOM (or HETATM) records.  

Although RasMol cannot generate symmetry-related molecules the 
RasMol-derived WebLab Viewer can use the CRYST1 information to do this.

WebLab Viewer (including a free 'Lite' version) can be obtained from:
 
          http://www.msi.com

As an alternative, if you have access to the UK Chemical Database 
Service (CDS), you can use the CDS utility program 'fillxr' to fill a 
unitcell or generate a 'block' of unitcells in .xr format and then 
use Babel to convert the coordinates to .pdb format. Although this is 
a bit cumbersome it does mean that all the structures in the CDS 
databases for metals (MDF), inorganic (ICSD), and 
organic/organo-metallic molecules (CSSR) can be viewed with RasMol/Chime.
 
Further info on the CDS can be obtained from:

          http://www.dl.ac.uk/CDS/cds.html

In my experience the above procedures certainly work although others 
may well be aware of other simpler methods. It would be very useful 
if RasMol/Chime/WebLab Viewer could directly read CDS CSSR (.xr) 
format files (something else to add to the wish list!).

Regards,

          Geoff

References: <0EXO00BT7WV8BI@rfd1.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: RasMol/Chime Venn
Date: Tue, 18 Aug 1998 10:37:38 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

OK, Thanks, I've updated the copy on my website.  As far as I can figure
out, Will McClure made a table in a version of the RasMol Manual which he
wrote, in which Tyr was shown as hydrophobic.  He makes a good point that
it is more hydrophobic than Ala, nevertheless of course the diagram should
reflect the behavior of RasMol and Chime.  I was unable to find any Tyr
error in the version of the manual on my site (rasman.htm) which I revised
from Sayle's original.

At 8/16/98, you wrote:
>Eric Martz wrote:
>> Hmmm.  My tests indicate that both RasMol and Chime consider Tyr to be
>> POLAR and not HYDROPHOBIC.
>
>Yes, you're right.
>At least it's made me tidy the picture up a bit - now all the groups are
>ovals.
>
>New (neater) version at http://inn-prot.weizmann.ac.il/download/venn.GIF
>
>Kurt
>
>-- 
>---------------------------------------------------------------
>Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
>Israeli National Node           
>Biological Computing Unit       Tel: +-972-8-9342614
>Weizmann Institute of Science   Fax: +-972-8-9466269
>Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
>---------------------------------------------------------------
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Is Chime 2 beta 4 solid?
Date: Wed, 26 Aug 1998 16:59:05 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Recently MDL replaced Chime 2 beta 3 (for Windows95/NT only) with beta 4.
I have been informed by Jean Holt at MDL that the ONLY change made since
beta 3 was 'chimestring authentication'. I have just gotten around to
trying beta 4 for the first time.  I spotted no changes since beta 3 in a
quick once thru one of each of the kinds of use I have made of Chime.

If anyone else has been using beta 4 for awhile and seen no differences,
I'd like to know that just as confirmation.  Of course if you have seen a
difference, please describe it in detail.

BTW, Jean gave me this explanation of the change.  I don't understand the
explanation but I don't seem to need to. I presume it concerns only the
interaction of Chime with Chemscape Server, which I never use. "A
Chimestring is the packet format in which we pass the molfile between 
the web client and the host. While the contents of a molfile are public 
domain, the Chimestring encapsulation is not."

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Andreas Bohne <a.bohne@dkfz-heidelberg.de> (by way of Eric Martz <emartz@microbio.umass.edu>)
Subject: PDB2MGIF
Date: Fri, 28 Aug 1998 11:08:26 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

At

http://www.dkfz-heidelberg.de/spec/pdb2mgif/
you can find a web service which converts pdb files into an animated gif
images. The images are rendered by a version of RasMol2.

With kind regards

Andreas
-- 
+---------------------------------------------------
| Dipl.-Inform.			
| Andreas Bohne			
| DKFZ-Heidelberg
| Zentrale Spektroskopie  -R0400-	
| AG: Mollecular Modeling
| Im Neuenheimer Feld 280	Tel: 06221 / 42-4541
| D-69120 Heidelberg 		Fax: 06221 / 42-2995
| E-Mail: a.bohne@dkfz-heidelberg.de

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Chime-saved scripts: access from javascript?
Date: Wed, 02 Sep 1998 14:00:37 -0400
To: "Dr. Greg Quinn" <greg@franklin.ljcrf.edu>
Cc: rasmol@dhcp-srv2.oit.umass.edu, jch@mdli.com

In Chime 2 but not Chime 1, the menu option "Edit, Copy chime script"
places the script on the clipboard. As best I can find out, javascript has
no access to the clipboard.  Therefore, what I recommend at present is that
the script be pasted into e.g. Wordpad or Word, and then written to disk.

If Chime/javascript had access to a Chime-generated script, it would be
possible to grab the script, load a new chime-containing document, then
execute the script, so as to preserve the PDB file and view.  This is
something which could be quite useful but I think it is not yet possible.
For example one could have a set of thumbnail Chimes, and by clicking on
one, it could enlarge to fill the entire window.

So I think an enhancement to enable Chime to send the script to a callback
function (and thereby to javascript) would be extremely useful.  I don't
recall this having come up before, which is why I'm copying this to the
person at MDLI who keeps track of Chime bug reports and enhancement
requests (Jean Holt).

There has been private discussion about enabling Chime (version 3?) to
write the script directly to a disk file, which I was told is possible.
(When you install a plugin, you give it permission to do as it will,
apparently.)  But don't hold your breath.

Incidentally, chime-generated scripts run fine in RasMol.  There are a
couple of chime commands which RasMol doesn't recognize but it goes past
them with a harmless error message.  An undocumented feature is that

#! command here

is ignored by rasmol but executed by chime, while in

command here ## comment

the command is executed in rasmol but not in chime.  (I'm not quite sure I
have the syntax correct as I'm drawing from memory.) However this
capability has had no significant use to my knowledge.  It would make sense
to preface the chime-only commands which chime writes into its scripts with
#! but it is very low priority.

At 9/2/98, you wrote:
>Hi Dr. Martz;
>Apologies for troubling you but I can not find the answer written
>anywhere and your experience in this area is great; is there a way to
>get the CHIME plugin to dump via javascript and a callback, a rasmol
>script representing the current view? This rasmol script dump needs to
>be dealt with in the javascript code, that's why it needs to be a
>callback and not a file dump (as you can do with rasmol with the 'write'
>command).
>
>Thansk for any clues
>
>Greg Quinn
>
>-- 
>*****************************************
>Computational Biology Group
>The Burnham Institute
>(formerly La Jolla Cancer Research Inst.)
>12901 North Torrey Pines road
>La Jolla
>CA92037
> 
>Phone:(619) 646 3103
>Email: greg@franklin.ljcrf.edu
>http://franklin.ljcrf.edu/greg
>http://www.greg.com/
>*****************************************
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: "Jesus M. Sanz" <jmsanz@umh.es>
Subject: Help requested
Date: Thu, 10 Sep 1998 18:13:43 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Dear friends,

	I am about to finish a small www page for my students (and the
rest of the world outside) using Chime. It is only in Spanish for the
moment, but I promise to create a twin one in English as soon as this works.

	Some weeks ago I requested your help about how to configure our web server 
for the different MIME types (I was really ashamed when someone pointed me
to the FAQ! which actually I did not read properly). Now, I need your help
again.

	When accessing the page on-line, I cannot load neither the scripts nor 
a series of pages that allow the loading of pdb files showing secondary
structure elements as well as complete proteins, etc... I guess there must
be some
problem with the javascripts, as the .js files are not recognized. I
included the next string in the registry file of our server
(for Microsoft Internet Information Server):

				application/x-javascript,js,,5

(although this is not defined in the Chime FAQ file) but still it does not
work.

	Maybe you can see it clearer if you try to navigate through the page:

			http://18597.umh.es/jmsanz/Inicio.htm

	Could anyone, please, give me some indications? Any help will be
greatly acknowledged.

	By the way, do use Netscape 3.0 and Chime 1.0, as I included old
downloadable tutorials and I have had not time to renew them. 
Also, note that I still have not written the Copyrights and all that.

	Thanks very much indeed in advance

	Jesus Sanz

--------------------------------------------------------------------------
Prof. Jesus M. Sanz				Tel:(34) 966 658 761
Dep. Bioquimica y Biologia Molecular		Fax:(34) 966 658 780
Universidad Miguel Hernandez			E-mail: jmsanz@umh.es
c/ Monovar s/n, Poligono Carrus, ELCHE, 03206-Alicante, SPAIN
       "Asombrarse es la esencia de la vida"   M. C. Escher
--------------------------------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: New Chime Beta 1 for Macintosh PowerPC from MDL
Date: Thu, 10 Sep 1998 16:38:04 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

This Message was sent to the RasMol list by MDLI but didn't get thru.
It was forwarded by Eric Martz to circumvent technical difficulties.

>From: New Chime <chime-feedback@mdli.com>
>To: "'rasmol@lists.umass.edu'"
>Subject: New Chime Beta 1 for Macintosh PowerPC from MDL
>Date: Thu, 10 Sep 1998
>
>Dear Chime(tm) User,
>
>Thank you for choosing Chime for your Intranet and Internet applications.
>
>The Beta version of Chime 2.0 is available for the Macintosh PowerPC.  This 
>major release has many enhancements which include:
>
>  * New Chime menus
>  * Transfer to ISIS/Draw 2.1.3 and above
>  * Calculation of charges on atoms
>  * Log P calculations
>  * Interactive modeling
>  * Rendering of Rgroups and Polymers
>  * Rendering of ISIS 3D query feature display in the 3D layer
>  * Support for Gaussian Cube File (.cub, .cube)
>  * Support for Rasmol Script File (.scr)
>  * Sprout Hydrogens
>  * Color Amino Acids
>
>We plan to add the following features for the final Chime 2.0 release 
>scheduled for November, 1998:
>
>  * Integrated JCAMP-DX reader and viewer using code licensed from the 
>    University of West Indies, Mona Jamaica for importing spectra
>  * Support for JCAMP-DX File (.jdx, .dx)
>  * JavaScript via LiveConnect
>  * Copy Chime Script
>  * Support for MDL Sketch File (platform specific) (.skc)
>
>As a Beta release, Chime 2.0 Beta is not intended for use in a production 
>environment.  The Beta test period will run from September 4, 1998 until 
>September 25, 1998, at which time MDL will begin final preparation for the 
>release scheduled for November, 1998.  Please report any program defects 
>promptly to your MDL Technical Support Specialist.  Enhancement requests 
>will be considered for future releases.
>
>Chime software and documentation are delivered via the MDL Information 
>Systems, Inc. (MDL) web site.  To access the products, installation 

>instructions, and technical materials, please use your web browser to 
>connect to one of the following URLs:
>
>  * http://www.mdli.com/download
>  * http://www-uk.mdli.com/download
>
>Read the instructions on the web pages to download and install your 
>software.  Please check the MDL web site regularly since release notes, 
>documentation and future updates of Chime will be delivered from that 
>location.
>
>We greatly appreciate your time and efforts in testing Chime in your 
>computing environment and look forward to your comments.
>
>
>Sincerely,
>
>
>The Chime Team
>MDL Information Systems, Inc.

X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id WAA22136
++++------+------+------+------+------+------+------+------+------+------+
From: Rick Lee <rick@sciencemedia.com>
Subject: Atomic radii
Date: Thu, 10 Sep 1998 19:02:56 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

Hi all.,

I've looked through the RasMol online docs, and I can't find the values
of atomic radii that Chime uses when it renders using Spacefill.

Where can I find that list?

Thanks,
Rick

********************************************
*  Richard H. Lee, PhD
*  Editor/Lead Scientist, Biochemistry
*  rick@sciencemedia.com
*
*  ScienceMedia, Inc.
*  6540 Lusk Blvd., Suite C148
*  San Diego, CA 92121-2767
*
*  TEL: 619/625-9261, Ext. 7
*  FAX: 619/625-9262
*
*  http://www.sciencemedia.com
*********************************************  

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Chime 2 b4 installer
Date: Fri, 11 Sep 1998 09:29:46 -0400
To: "Raymond D. Mosteller" <rmostell@hsc.usc.edu>
Cc: rasmol@dhcp-srv2.oit.umass.edu

During the past week, MDLI staff have confirmed that the Chime installers
on MDLI's website were corrupted. I have been told by Franklin Adler at
MDLI that they are now fixed.  Please download the installer again.  If you
have further problems, please contact
chime-feedback@mdli.com

At 9/10/98, you wrote:
>Dr. Martz,
>I have a problem installing Chime 2 beta 4 (ch2b4w32.exe) on my machine
>(Win98, NS 4.04, Chime 2 beta 2 already installed). I get the following
>InstallShield error message (NS and all other Windows programs closed):
>
>"The decompression of %s failed. There may not be enough free disk space
>available in the TEMP file."
>
>I have 413 Mb available on drive C (2 Gb). After attempting to install, I
>found 2 files (Data.tag and Data1.cab) in C:\windows\temp directory. I am
>still able to rerun the older beta 2 installer at this time.
>
>My daughter at Tulane gets the same message on her Compaq Laptop (Win95, NS
>?.?) when trying to install Chime 2 beta 4.
>
>Can you help us?
>
>Thanks,
>Ray Mosteller
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Future of the PDB
Date: Fri, 11 Sep 1998 13:10:37 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

For those who haven't heard, the US government agencies which fund the
Protein Data Bank (DOE, PHS, NSF) required a competition in summer 1998 for
funding renewal (a requirement announced in 1994).  In August 1998, it was
made known that the new award will go to a consortium headed by Helen
Berman at Rutgers U (New Brunswick NJ US).  The transfer of the Protein
Data Bank from Brookhaven National Lab where it has been since its
inception is scheduled to occur November 1, 1999.  More detail can be found
in the current issue of Science (vol 281, Sept. 11, 1998, pp. 1584-1585).
In brief, there is concern in some quarters of the scientific community
about maintaining the quality and reliability of the PDB. The award was
said to be based not on quality of past performance but on plans for the
future. Mary Clutter at NSF plans to release details about the plans of the
successful application soon, which will help to clarify the situation.

-Eric Martz

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <3.0.3.32.19980910181343.00692708@mussol.umh.es>
++++------+------+------+------+------+------+------+------+------+------+
From: Alexander Garcia <acad@accefyn.org.co>
Subject: Re: Help requested
Date: Sun, 13 Sep 1998 10:56:08 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Revisando su pagina encontre esto aque depronto le resulta interesante:

JavaScript Error: http://18597.umh.es/jmsanz/adna1.htm, line 56:

sendRasmolScriptToChime is not defined.

Actualmente estoy escribiendo un libro acerca de usos de computadores en
biologia, le interesaria havcerse cargo del capitulo de rasmol y chime?

Jesus M. Sanz wrote:

> Dear friends,
>
>         I am about to finish a small www page for my students (and the
>
> rest of the world outside) using Chime. It is only in Spanish for the
> moment, but I promise to create a twin one in English as soon as this
> works.
>
>         Some weeks ago I requested your help about how to configure
> our web server
> for the different MIME types (I was really ashamed when someone
> pointed me
> to the FAQ! which actually I did not read properly). Now, I need your
> help
> again.
>
>         When accessing the page on-line, I cannot load neither the
> scripts nor
> a series of pages that allow the loading of pdb files showing
> secondary
> structure elements as well as complete proteins, etc... I guess there
> must
> be some
> problem with the javascripts, as the .js files are not recognized. I
> included the next string in the registry file of our server
> (for Microsoft Internet Information Server):
>
>                                 application/x-javascript,js,,5
>
> (although this is not defined in the Chime FAQ file) but still it does
> not
> work.
>
>         Maybe you can see it clearer if you try to navigate through
> the page:
>
>                         http://18597.umh.es/jmsanz/Inicio.htm
>
>         Could anyone, please, give me some indications? Any help will
> be
> greatly acknowledged.
>
>         By the way, do use Netscape 3.0 and Chime 1.0, as I included
> old
> downloadable tutorials and I have had not time to renew them.
> Also, note that I still have not written the Copyrights and all that.
>
>         Thanks very much indeed in advance
>
>         Jesus Sanz
>
> ------------------
> -------------------------------------------------------
> Prof. Jesus M. Sanz                             Tel:(34) 966 658 761
> Dep. Bioquimica y Biologia Molecular            Fax:(34) 966 658 780
> Universidad Miguel Hernandez                    E-mail: jmsanz@umh.es
> c/ Monovar s/n, Poligono Carrus, ELCHE, 03206-Alicante, SPAIN
>        "Asombrarse es la esencia de la vida"   M. C. Escher
> -----------------------------------------------------------
> --------------

++++------+------+------+------+------+------+------+------+------+------+
From: "Brian White" <brian.white@umb.edu>
Subject: Chime question
Date: Mon, 14 Sep 1998 10:31:47 -0500
To: rasmol <rasmol@dhcp-srv2.oit.umass.edu>

Two questions:

(1) Does anyone know a way to disable the pop-up menus in chime - I'm
using it in a teaching lab & would like to have the students identify
the amino acids by structure, not by label.

(2) I would like to make a "rasmol simulator" in chime - with a command
line interface & ability to show the messages that chime generates
(especially the identity of atoms clicked). I can see how to do this,
but has anyone else done it? I'd like to give my students the ability to
do rasmol-like work without haveing to download rasmol as well as chime.

Brian

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Chime question
Date: Mon, 14 Sep 1998 11:10:14 -0400
To: brian.white@umb.edu
Cc: rasmol@dhcp-srv2.oit.umass.edu

At 9/14/98, Brian White wrote:
>Two questions:
>
>(1) Does anyone know a way to disable the pop-up menus in chime - I'm
>using it in a teaching lab & would like to have the students identify
>the amino acids by structure, not by label.

This question is best answered by someone at MDL. There may be a way in
Chime 2 but I'm not certain.

>(2) I would like to make a "rasmol simulator" in chime - with a command
>line interface & ability to show the messages that chime generates
>(especially the identity of atoms clicked). I can see how to do this,
>but has anyone else done it? I'd like to give my students the ability to
>do rasmol-like work without haveing to download rasmol as well as chime.

I am nearing completion and release of exactly this.  I have a version
which works with Chime 1 which I'll be happy to provide to you in
pre-release, as is, if you don't want to wait a few more weeks. This will
be the first portion to be released of a more ambitious project I'm working
on called the 'Protein Explorer'.

I'm trying to support multi-model NMR files and there are some issues about
Chime 1 vs. Chime 2 which I'm working on, as well as documentation to
finish.  One of the nice features which seems to work fine is you can type
a 4-character PDB ID code into the load slot and fetch the PDB file thru
the Internet from the PDB; or of course you can load a PDB file from your
local hard disk. Another nice mode is a 'protein comparator': two Chime's
with ability to load and manipulate two molecules independently side by side.

There are examples of how to do the javascript for this which have been on
my site for many months under 'Command-line demonstration for Chime',
http://www.umass.edu/microbio/chime/chimehow/fs_cmdln.htm
but I recommend that you get the Protein Explorer version instead at this
point.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <199809110205.CAA09680@vmail.connectnet.com>
++++------+------+------+------+------+------+------+------+------+------+
From: Orjan Hansson <Orjan.Hansson@bcbp.gu.se>
Subject: Re: Atomic radii
Date: Tue, 15 Sep 1998 16:57:18 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Rick Lee wrote:
> 
> I've looked through the RasMol online docs, and I can't find the
> values
> of atomic radii that Chime uses when it renders using Spacefill.
> 
> Where can I find that list?
> 

I also needed that info so I looked into the RasMol source code, which
is available at
http://www.glaxowellcome.co.uk/software/down.html

I found the following structure in the file abstree.h:
typedef struct {
           char symbol[2];
           int covalrad;
           int vdwrad;
           int cpkcol;
           char *name;
        } ElemStruct;

A bit further down in the file there is a definition of an array Element
of such structures. The following is copy of a few of the lines:
ElemStruct Element[MAXELEMNO] =  {
    { { ' ', ' ' }, 170, 360, 12, ""             },  /*   0 */
    { { 'H', ' ' },  80, 275,  4, "HYDROGEN"     },  /*   1 */
    { { 'H', 'e' }, 400, 550,  5, "HELIUM"       },  /*   2 */
    { { 'L', 'i' }, 170, 305, 14, "LITHIUM"      },  /*   3 */
    { { 'B', 'e' },  88, 157, 12, "BERYLLIUM"    },  /*   4 */
    { { 'B', ' ' }, 205, 387, 13, "BORON"        },  /*   5 */
    { { 'C', ' ' }, 170, 387,  0, "CARBON"       },  /*   6 */
    { { 'N', ' ' }, 188, 350,  1, "NITROGEN"     },  /*   7 */
    { { 'O', ' ' }, 182, 337,  2, "OXYGEN"       },  /*   8 */
    { { 'F', ' ' }, 180, 325,  6, "FLUORINE"     },  /*   9 */
    { { 'N', 'e' }, 280, 505, 12, "NEON"         },  /*  10 */
/* (lines deleted) */
    { { 'N', 'o' }, 212, 397, 12, "NOBELIUM"     },  /* 102 */
    { { 'L', 'r' }, 210, 395, 12, "LAWRENCIUM"   }   /* 103 */ /* Lw? */
        };
I'm not completely sure, but I think that this is the internal database
that RasMol uses when rendering atoms.

Since a single RasMol unit corresponds to 1/250th of an Angstrom, we get
for e.g. oxygen: 337/250 = 1.35 Angstom.

Regards, Orjan
 
*****************************************
Orjan Hansson
Biochemistry and Biophysics
Department of Chemistry
Goteborg University and
Chalmers University of Technology
P.O. Box 462
SE-405 30 GOTEBORG (Sweden)
Phone: (+46) 31 773 3929
Fax: (+46) 31 773 3910
http://www.bcbp.gu.se/~orjan
*****************************************

++++------+------+------+------+------+------+------+------+------+------+
From: Steven Verhey <verhey@elwha.evergreen.edu>
Subject: Re: Chime question
Date: Tue, 15 Sep 1998 08:21:18 -0700 (PDT)
To: Brian White <brian.white@umb.edu>
Cc: rasmol <rasmol@dhcp-srv2.oit.umass.edu>

I don't know anything about question (2), but can suggest a (somewhat 
laborious) approach to (1) which works with rasmol.  I don't see why it 
wouldn't work for chime as well.

The .pdf files contain the three-letter amino acid code corresponding to 
each atom displayed.  If you edit this field to read, say, "xxx," the 
program reports xxx as the name of the residue containing the atom.  To 
make it easier to edit files this way, I  discard atoms relating to 
most of a protein, saving only an alpha helix, for example.  This also 
makes it easier for the students to focus on the details at hand.  If you 
do this to two helices (or sheets, or whatever), you can use one in class 
and the other for an exam.

Steve Verhey
The Evergreen State College

On Mon, 14 Sep 1998, Brian White wrote:

> Two questions:
> 
> (1) Does anyone know a way to disable the pop-up menus in chime - I'm
> using it in a teaching lab & would like to have the students identify
> the amino acids by structure, not by label.
> 
> (2) I would like to make a "rasmol simulator" in chime - with a command
> line interface & ability to show the messages that chime generates
> (especially the identity of atoms clicked). I can see how to do this,
> but has anyone else done it? I'd like to give my students the ability to
> do rasmol-like work without haveing to download rasmol as well as chime.
> 
> Brian
> 
> 

References: <199809110205.CAA09680@vmail.connectnet.com>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Atomic radii
Date: Tue, 15 Sep 1998 11:40:57 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Thanks to Orjan Hansson for finding the atomic radii in RasMol's source code.
If someone wants to convert that table to Angstroms and post it to the list,
I'll put it on my website.

BTW, the source code for RasMol 2.6 beta 2a is also available at
http://www.umass.edu/microbio/rasmol/distrib/RasMol26b2.tar.gz

or as a set of plain text files at
ftp://www.bio.umass.edu/pub/shareware/rasmol/source_code/

You get to this from the RasMol Home Page by selecting 
RasMol, source code
or Index, Introduction, source code
or Index, Getting RasMol, source code

BTW#2: Roger Sayle did not provide distinguising version numbers within
RasMol itself. The version designations I have assigned are listed in the
chronology at
http://www.umass.edu/microbio/rasmol/getras.htm#rasverhist

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: "Fernando Gabriel Ranea  " <fgranea@microb.ffyb.uba.ar>
Subject: RasMol 2.6 Source Code
Date: Mon, 21 Sep 1998 18:28:54 ARG
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Rasmolers:

Where I can obtain the RasWin 2.6 Source Code? I have downloaded a source
code from GlaxoWellcome Home Page but it is the version 2.4/2.5 for Windows.
Sincerely,

Fernando Gabriel Ranea 
fgranea@microb.ffyb.uba.ar

++++------+------+------+------+------+------+------+------+------+------+
From: Judith Miller <jmiller@WPI.EDU>
Subject: printing RasMol images
Date: Tue, 22 Sep 1998 08:41:07 -0400 (EDT)
To: RasMol <rasmol@dhcp-srv2.oit.umass.edu>

Colleagues--

I'm new here, and my presence is prompted by a question.  I want to give
my freshman students an assignment using RasMol, and am considering
having them print images.  I can't get RasMol's File-Print command to
result in any action.  I checked the printer setup and it all looks
good.  Any suggestions?  I'm using RasMol 2.6 in Windows 95.

And, if I do get it printing, do you suggest that I switch to a white
background for the images?

Many thanks--

Judy Miller
Professor, Biology and Biotechnology
WPI
Worcester MA  01609
jmiller@wpi.edu

References: <Pine.OSF.4.02A.9809220840381.7755-100000@reno.WPI.EDU>
++++------+------+------+------+------+------+------+------+------+------+
From: Eblinger <f.eblinger@rz.uni-sb.de>
Subject: Re: printing RasMol images
Date: Tue, 22 Sep 1998 15:30:38 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

--------------50E7B0156984ED939DE1943E

Dear Judith,
 to get a white background enter the command: set background white.
One way to print rasmol images is to export eg as *.bmp file and insert it
eg in winword.
high resolution images are possible using the postscript export options;
you'll  need a postscript reader!

enjoy it

                Frank

Frank Eblinger
Universität des Saarlandes
Saarbrücken
f.eblinger@rz.uni-sb.de

Judith Miller schrieb:

> Colleagues--
>
> I'm new here, and my presence is prompted by a question.  I want to give
> my freshman students an assignment using RasMol, and am considering
> having them print images.  I can't get RasMol's File-Print command to
> result in any action.  I checked the printer setup and it all looks
> good.  Any suggestions?  I'm using RasMol 2.6 in Windows 95.
>
> And, if I do get it printing, do you suggest that I switch to a white
> background for the images?
>
> Many thanks--
>
> Judy Miller
> Professor, Biology and Biotechnology
> WPI
> Worcester MA  01609
> jmiller@wpi.edu

--------------50E7B0156984ED939DE1943E

<HTML>
Dear Judith,
<BR>&nbsp;to get a white background enter the command: <I>set background
white</I>.
<BR>One way to print rasmol images is to <B>export</B> eg as *.bmp file
and insert it eg in winword.
<BR>high resolution images are possible using the postscript export options;
you'll&nbsp; need a postscript reader!

<P>enjoy it

<P>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Frank
<BR>&nbsp;

<P>Frank Eblinger
<BR>Universit&auml;t des Saarlandes
<BR>Saarbr&uuml;cken
<BR>f.eblinger@rz.uni-sb.de

<P>Judith Miller schrieb:
<BLOCKQUOTE TYPE=CITE>Colleagues--

<P>I'm new here, and my presence is prompted by a question.&nbsp; I want
to give
<BR>my freshman students an assignment using RasMol, and am considering
<BR>having them print images.&nbsp; I can't get RasMol's File-Print command
to
<BR>result in any action.&nbsp; I checked the printer setup and it all
looks
<BR>good.&nbsp; Any suggestions?&nbsp; I'm using RasMol 2.6 in Windows
95.

<P>And, if I do get it printing, do you suggest that I switch to a white
<BR>background for the images?

<P>Many thanks--

<P>Judy Miller
<BR>Professor, Biology and Biotechnology
<BR>WPI
<BR>Worcester MA&nbsp; 01609
<BR>jmiller@wpi.edu</BLOCKQUOTE>
&nbsp;</HTML>

--------------50E7B0156984ED939DE1943E--

References: <Pine.OSF.4.02A.9809220840381.7755-100000@reno.WPI.EDU>
++++------+------+------+------+------+------+------+------+------+------+
From: "John J. Stezowski" <jjs@unlinfo.unl.edu>
Subject: Re: printing RasMol images
Date: Tue, 22 Sep 1998 08:36:22 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Judith,
I usually do this be exporting a bitmap image and then import it into word
or paint and print.

Judith Miller wrote:

> Colleagues--
>
> I'm new here, and my presence is prompted by a question.  I want to give
> my freshman students an assignment using RasMol, and am considering
> having them print images.  I can't get RasMol's File-Print command to
> result in any action.  I checked the printer setup and it all looks
> good.  Any suggestions?  I'm using RasMol 2.6 in Windows 95.
>
> And, if I do get it printing, do you suggest that I switch to a white
> background for the images?
>
> Many thanks--
>
> Judy Miller
> Professor, Biology and Biotechnology
> WPI
> Worcester MA  01609
> jmiller@wpi.edu

References: <Pine.OSF.4.02A.9809220840381.7755-100000@reno.WPI.EDU> <3607A67E.B407DBD8@rz.uni-sb.de>
++++------+------+------+------+------+------+------+------+------+------+
From: Eblinger <f.eblinger@rz.uni-sb.de>
Subject: Selection of the active centre
Date: Tue, 22 Sep 1998 16:38:53 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Hi Rasmol users,

Does anybody know a simple procedure to select certain parts of an
enzyme?
Is there any "sphere command"? Is it possible to select amino acids in
a sphere of lets say 15 angstr. diameter around a metal ion or do I have
to do this boring job manually?

Thanks for your help in advance

                                Frank

Frank Eblinger
Universität des Saarlandes
Saarbrücken
f.eblinger@rz.uni-sb.de

References: <Pine.OSF.4.02A.9809220840381.7755-100000@reno.WPI.EDU> <3607A67E.B407DBD8@rz.uni-sb.de> <3607B67C.2DDD4DF8@rz.uni-sb.de>
++++------+------+------+------+------+------+------+------+------+------+
From: "Dr. Kurt Giles" <kurt@inn-prot.weizmann.ac.il>
Subject: Re: Selection of the active centre
Date: Tue, 22 Sep 1998 10:48:09 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

> Does anybody know a simple procedure to select certain parts of an
> enzyme?
> Is there any "sphere command"? Is it possible to select amino acids in
> a sphere of lets say 15 angstr. diameter around a metal ion or do I have
> to do this boring job manually?

Use the 'within' command with select or restrict, e.g.

select within (3.0, ligand)

selects all atoms within 3.0A of the ligand.
'Ligand' can be replaced by an atom or residue definition. You must use a
decimal point in the distance, otherwise it takes it to mean RasMol units
(i.e. 1/250 Angstrom)

Kurt

---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +972-8-9342614
Weizmann Institute of Science   Fax: +972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------
Currently at: Protein Data Bank, Brookhaven National Laboratory
              Tel: +1-516-344-2261  Fax: +1-516-344-5751

++++------+------+------+------+------+------+------+------+------+------+
From: Duane Sears <sears@lifesci.ucsb.edu>
Subject: Re: printing RasMol images
Date: Tue, 22 Sep 1998 09:38:59 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

Judy,

I have not systematically tested all of the various ways for printing
RasMol images, but I discovered some time ago that RasMol images that have
been copied (with RasMol's pulldown Edit/Copy command) and pasted into Word
documents yield extraordinarily good images for printing with a laser
printer.  While I've never tried printing these images with a color
printer, I expect the color images would be pretty good if the black and
white images are any indication.

Duane

At 08:41 AM 9/22/98 -0400, you wrote:
>Colleagues--
>
>I'm new here, and my presence is prompted by a question.  I want to give
>my freshman students an assignment using RasMol, and am considering
>having them print images.  I can't get RasMol's File-Print command to
>result in any action.  I checked the printer setup and it all looks
>good.  Any suggestions?  I'm using RasMol 2.6 in Windows 95.
>
>And, if I do get it printing, do you suggest that I switch to a white
>background for the images?
>
>Many thanks--
>
>Judy Miller
>Professor, Biology and Biotechnology
>WPI
>Worcester MA  01609
>jmiller@wpi.edu
>
>
>
>
__________________________________________________________
Professor Duane W Sears
Department of Molecular, Cellular and Developmental Biology
University of California
Santa Barbara, CA 93106

Phones:

805-893-3499 (Office)  805-893-4272(Lab)  805-893-4724(FAX)

E-mail:  sears@lifesci.ucsb.edu

Instructional web sites @  

  Immunology --   http://mentor.lscf.ucsb.edu/mcdb133/    
  Biochemistry --  http://mentor.lscf.ucsb.edu/mcdb108a/

References: <3.0.1.32.19980922093859.006e25f4@lifesci.ucsb.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: shoba <shoba@angis.usyd.edu.au>
Subject: Re: printing RasMol images
Date: Wed, 23 Sep 1998 09:09:16 +1000
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Judy,

I second what Duane Sears says. In Rasmol 2.5.1, I use File/Clipboard
and then in Word, I prefer Edit/Paste Special and choose the Device
Independent Bitmap for better printed images.

The alternative would be to use Rasmol's Export/EPSF and make an EPS
file, which Word can read using Insert/Picture/From file.

BTW Rasmol's Export/GIF is excellent for making html images quickly.

Shoba

Duane Sears wrote:
> 
> I have not systematically tested all of the various ways for printing
> RasMol images, but I discovered some time ago that RasMol images that have
> been copied (with RasMol's pulldown Edit/Copy command) and pasted into Word
> documents yield extraordinarily good images for printing with a laser
> printer.  

=======================================================================
Shoba Ranganathan, Ph D                             Tel:+61-2-9351-1870
ANGIS, Bay 16, Suite 104                        Toll free:1-800-728-028
Australian Technology Park                          Fax:+61-2-9351-1878
Eveleigh NSW 1430
Australia                 Personal URL: http://seal.angis.org.au/~shoba
================MolMod Home Page: http://molmod.angis.org.au===========

	charset="iso-8859-1"
X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id KAA24219
++++------+------+------+------+------+------+------+------+------+------+
From: "PENUELAS SANCHEZ, Ivan" <ipenuelas@unav.es>
Subject: RE: printing RasMol images
Date: Wed, 23 Sep 1998 16:28:40 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Judith,
I usually use the export/GIF option and then import the image to
programs like powerpoint to generate great looking slides for my
classes. Color copies in paper are always of lower quality, but also
give very good results.
	
	Iván

++++------+------+------+------+------+------+------+------+------+------+
From: SKG <skg@asis.com>
Subject: RE: printing RasMol images
Date: Wed, 23 Sep 1998 10:57:35 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

Color copies in paper are always of lower quality, but also
>give very good results.

Not nessecarily - with a good printer and a special ink cartridge & special
paper (photo grade) you can get almost photograph quality printouts. The
paper's expensive though (about $1/sheet!)
- - - - - - - - - - - -
_ _ _ _ _ _ _ _ _

Steven K. Gill

"Against the ruin of the world there is only one defense - the creative
act."  Kenneth Rexroth

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: NMR models in Chime: features and bug
Date: Wed, 23 Sep 1998 17:18:06 -0400
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: FranklinA@mdli.com, jch@mdli.com, tim@mind.net

Dear Chimeleons:

I have been developing a RasMol-like interface for Chime which I expect to
publish on my website soon (the "Protein Explorer").  One capability I am
including is the ability to load multiple-model NMR PDB files; to view all
models overlayed, or any one model at random.  (You can already see this
capability nicely displayed IF YOU ARE RUNNING CHIME 2 BETA 4 FOR WINDOWS
at http://www.umass.edu/microbio/chime/morpher/index.htm by selecting
calmodulin, apo-flexibility.)

Here are some of my conclusions about Windows 95/NT Chime 1.02 vs. 2 beta 4
for NMR data.  If anyone has found different or further results I'd like to
hear from them.

1. The RasMol manual 2.6-beta-2a
(http://www.umass.edu/microbio/rasmol/distrib/rasman.htm) states that when
a PDB file is loaded "load nmrpdb filename.pdb", the command "select
model=1" (where 1 is any valid model number) is available.  As far as I can
see this is not implemented in 2.6-beta-2a.  Maybe it was in an earlier
version and got broken? Or may be I put it in this version of the manual by
mistake? (I haven't dug up a version 2.5 manual to see if it is there too.)
RasMol displays the first model only, and can't seem to display multiple
models overlaid or any model after the first.

2. Chime 1 also does not support the "select model=1" command and behaves
as does RasMol.

3. Chime 2 beta 4 supports "select model=1" commands. The initial display
shows all models overlaid. The <embed> tag which invokes chime must include
"nmrpdb=1".  Although the RasMol manual suggests "load nmrpdb
filename.pdb", the "nmrpdb" seems to have no effect in the load command.

4. Despite invocation with 'nmrpdb=1', when a non-NMR file (having only a
single model and lacking MODEL N/ENDMDL records) is loaded, everything
seems to work except that not surprisingly, if you 'select model=1' you get
no atoms selected.  Therefore, a nice strategy would be to invoke with
'nmrpdb=1' regardless of whether single-model or NMR-style PDB's are to be
loaded EXCEPT FOR THE FOLLOWING BUG.

5. Chime 2 beta 4 has this bug: when invoked with nmrpdb=1, no script DISK
FILES will be properly executed. Script strings sent to Chime via immediate
mode buttons or via LiveConnect execute fine provided they don't call any
script FILES. Calling a script DISK FILE causes the image to disappear and
also the frank to disappear. (This bug has been reported some weeks ago to
the Chime development team at MDL.)

If anyone has anything to add to this please speak out!
-Eric
 

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Chime 2b1 for Macintosh: version detection vs. NCB Finder/Morpher
Date: Wed, 23 Sep 1998 17:34:50 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Recently MDL provided Chime version 2 beta 1 on their website. Several
people reported to me that the javascript tests I use on my site fail to
detect that this is Chime 2. (These tests are employed only for my
Noncovalent Bond Finder and Protein Morpher which require Chime 2.)

Franklin Adler at MDL has clarified that there is a problem in Macintosh
Navigator 4.0x in that javascript cannot retrieve the plugin identification
string from Chime (navigator.plugins[i].name), which is how I normally test
for the version number.  At present no workaround is known. What is
available on the Mac is only the filename of the Chime application file.
Perhaps MDL will put the version number in the filename for the next Mac
release.

(In fact, Chime 2 beta 1 for Macintosh does not yet implement LiveConnect,
which is also required for the above two-mentioned resources at my website.
We'll have to wait for a later beta to be able to use these resources on
the Mac.)

In case anyone else depends on version detection, I thought the above info
might be of interest.
-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: NMR models in Chime: features and bug
Date: Wed, 23 Sep 1998 18:49:21 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Thanks to Roger Sayle, I stand corrected on point #1 in my message of this
subject. RasMol 2.6 beta 2 a handles multiple NMR models beautifully! (I
probably just forgot to load from the command line using 'load nmrpdb
filename.pdb').

I have verified that I still cannot get Chime 1 to handle NMR data as
multiple models (with nmrpdb=1 in the embed tag and despite 'load nmrpdb
filename.pdb'). So the behavior I described for RasMol (incorrectly) does
appear to be correct for Chime 1.

No corrections (so far) for the remaining points #2-#5.

Apologies to Roger!
-Eric

References: <Pine.OSF.4.02A.9809220840381.7755-100000@reno.WPI.EDU>
 <3607A67E.B407DBD8@rz.uni-sb.de>
X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id TAA26935
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Selection of the active centre
Date: Wed, 23 Sep 1998 19:12:31 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

At 9/22/98, you wrote:
>Hi Rasmol users,
>
>Does anybody know a simple procedure to select certain parts of an
>enzyme?
>Is there any "sphere command"? Is it possible to select amino acids in
>a sphere of lets say 15 angstr. diameter around a metal ion or do I have
>to do this boring job manually?
>
>Thanks for your help in advance
>
>                                Frank
>
>
>Frank Eblinger
>Universität des Saarlandes
>Saarbrücken
>f.eblinger@rz.uni-sb.de

Dr. Eblinger: my Noncovalent Bond Finder
(http://www.umass.edu/microbio/chime/find-ncb/index.htm) makes exactly this
task very easy, and shows the results very clearly. Basically it provides a
lot of shortcut buttons to automate the use of the 'within' command.  In
fact, for the typical metal, it finds the coordinating atoms in a single
click, and then fills out and identifies the amino acids in one click per
AA. Unfortunately you can use it only if you have a Windows95/NT system
since Chime 2 is not yet available for Macintosh and will not be provided
for SGI. 

Regards, -Eric Martz

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: nell@ppe.curtin.edu.au (Eleanor Morgan)
Subject: Re: NMR models in Chime: features and bug
Date: Thu, 24 Sep 1998 08:51:09 +0800
To: rasmol@dhcp-srv2.oit.umass.edu

Hi Rasmolians and Chimolians,

>Here are some of my conclusions about Windows 95/NT Chime 1.02 vs. 2 beta 4
>for NMR data.  If anyone has found different or further results I'd like to
>hear from them.
>
>1. The RasMol manual 2.6-beta-2a
>(http://www.umass.edu/microbio/rasmol/distrib/rasman.htm) states that when
>a PDB file is loaded "load nmrpdb filename.pdb", the command "select
>model=1" (where 1 is any valid model number) is available.  As far as I can
>see this is not implemented in 2.6-beta-2a.  Maybe it was in an earlier
>version and got broken? Or may be I put it in this version of the manual by
>mistake? (I haven't dug up a version 2.5 manual to see if it is there too.)
I am using Rasmol v2.6-beta-2a on a Macintosh and this feature works just
fine, in fact we have used it in a few of our student computing practicals
- we use Rasmol quite a bit with our Biochemistry students.

Regards,
Eleanor Morgan

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Eleanor (Nell) Morgan            |  nell@ppe.curtin.edu.au
Technical Officer/Web Coordinator|  tstainba@cc.curtin.edu.au
School of Biomedical Sciences    |  Phone:    (61)(08) 9266 4369 (wk)
Curtin University of Technology  |            (61)(08) 9528 7445 (hm)
GPO Box U1987, Perth,            |  Fax:      (61)(08) 9266 2342
Western Australia 6845           |
http://www.curtin.edu.au/curtin/dept/biomed/teach/biochem/nhome.html

                                       _--_|\
                                      /      \
                         >>>------->  \_.--._/
                                            ^
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

	charset="iso-8859-1"
X-MSMail-Priority: Normal
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4
++++------+------+------+------+------+------+------+------+------+------+
From: "Andrew Fellowes" <molpath@chmeds.ac.nz>
Subject: Re: Selection of the active centre
Date: Thu, 24 Sep 1998 13:12:41 +1200
To: <rasmol@dhcp-srv2.oit.umass.edu>, <rasmol@dhcp-srv2.oit.umass.edu>

But it doesn't seem to work in Internetr Explorer 4.01

-----Original Message-----
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Selection of the active centre
Date: Thursday, 24 September 1998 11:12
To: rasmol@dhcp-srv2.oit.umass.edu <rasmol@dhcp-srv2.oit.umass.edu>

At 9/22/98, you wrote:
>Hi Rasmol users,
>
>Does anybody know a simple procedure to select certain parts of an
>enzyme?
>Is there any "sphere command"? Is it possible to select amino acids in
>a sphere of lets say 15 angstr. diameter around a metal ion or do I have
>to do this boring job manually?
>
>Thanks for your help in advance
>
>                                Frank
>
>
>Frank Eblinger
>Universität des Saarlandes
>Saarbrücken
>f.eblinger@rz.uni-sb.de

Dr. Eblinger: my Noncovalent Bond Finder
(http://www.umass.edu/microbio/chime/find-ncb/index.htm) makes exactly this
task very easy, and shows the results very clearly. Basically it provides a
lot of shortcut buttons to automate the use of the 'within' command.  In
fact, for the typical metal, it finds the coordinating atoms in a single
click, and then fills out and identifies the amino acids in one click per
AA. Unfortunately you can use it only if you have a Windows95/NT system
since Chime 2 is not yet available for Macintosh and will not be provided
for SGI.

Regards, -Eric Martz

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Alexander Garcia <acad@accefyn.org.co>
Subject: Using Rasmol in VB
Date: Thu, 24 Sep 1998 15:16:29 -0500
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

Hi there! I am trying with Rasmol sourcecode for Visual Basic but I have
some problems with the link with Raswin, the program can't start Raswin.
I am using VB version 2.5 and Raswin version 2.4.
Are the versions the problem? Please, somone can help me?
Thanks a lot in advanced.

Sincerily,
Jael García


END OF 98.07-10
Beginning Oct 1, 1998:
++++------+------+------+------+------+------+------+------+------+------+
From: Evan P Kransdorf <epk8c@unix.mail.virginia.edu>
Subject: Chime and CGI
Date: Fri, 2 Oct 1998 13:21:14 -0400 (EDT)
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: emartz@microbio.umass.edu

Dear Chime-users,
  
   I am developing a web site for real-time viewing of output from a
molecular dynamics program.  I am using CHIME for the viewing of the
structures.  I am using a CGI script to generate the HTML dynamically. 
However, I am getting errors when I embed the chime in my HTML files. 
Specifically, when you load up the page it tell you that you need to
download the plugin.  I suspect that there is a header problem with my
CGI. Thanks in advance!

PS: I tried to look at the MDLI Chime FAQ but couldn't find it.

Evan Kransdorf
evan@virginia.edu

References: <Pine.A41.3.96.981002131752.85846A-100000@node5.unix.Virginia.EDU>
++++------+------+------+------+------+------+------+------+------+------+
From: Adrian Lee <alee@chem.utoronto.ca>
Subject: Re: Chime and CGI
Date: Fri, 02 Oct 1998 15:09:06 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Do you have two copies of Netscape.  Check where the plug-in is installed
if and only if you have two versions of Netscape.

Evan P Kransdorf wrote:

> Dear Chime-users,
>
>    I am developing a web site for real-time viewing of output from a
> molecular dynamics program.  I am using CHIME for the viewing of the
> structures.  I am using a CGI script to generate the HTML dynamically.
> However, I am getting errors when I embed the chime in my HTML files.
> Specifically, when you load up the page it tell you that you need to
> download the plugin.  I suspect that there is a header problem with my
> CGI. Thanks in advance!
>
> PS: I tried to look at the MDLI Chime FAQ but couldn't find it.
>
> Evan Kransdorf
> evan@virginia.edu

++++------+------+------+------+------+------+------+------+------+------+
From: SKG <skg@asis.com>
Subject: image in script file
Date: Sun, 04 Oct 1998 11:23:22 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

   Hi all - Could someone please tell me what the trick is to placing text
in a rasmol script? For instance, one is writing a tutorial & wants a title
page or a pdb file that will create this illusion.
Thank you kindly.................
- - - - - - - - - - - -
_ _ _ _ _ _ _ _ _

Steven K. Gill

"Against the ruin of the world there is only one defense - the creative
act."  Kenneth Rexroth

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Protein Explorer beta available
Date: Sun, 04 Oct 1998 23:24:04 -0400
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: rhodes@usm.maine.edu, brian.white@umb.edu

I have made available a beta-test version of a new Chime resource, the
Protein Explorer, at

http://www.umass.edu/microbio/chime/beta/explorer/index.htm  It is not yet
publically linked to my Chime site, pending feedback and further testing.
It is not downloadable from the public location, but is from a private one
(see below). I would value feedback from anyone interested, especially
Macintosh users.

The Protein Explorer provides a RasMol-like interface in Chime.  It allows
you to load any PDB file from your disk or via Internet from the closest
mirror of the PDB, plus a command line and message box.

The Protein Explorer works with either Chime 1 or (on Windows 95/NT only at
present) Chime 2 but requires Navigator 4.04 or later.

It also provides some conveniences for exploration of NMR files containing
multiple models: buttons to display all models overlaid, or any one model.

Included is the Protein Comparator, which provides two adjacent Chime's
(one above the other), and the ability independently to load and manipulate
separate molecules into each one.

Documentation important for seasoned RasMol users is provided;
documentation which will be needed for beginners is not yet provided.
Water, if present, is initially displayed as low-density dot surfaces.

The Protein Explorer can be test-driven from the above URL.  If in addition
you wish to download these resources, they are available from

ftp://ftp.bio.umass.edu/pub/temporary/explorer/

Instructions for unpacking these EXE files on Macintosh are at

http://merckx.chem.amherst.edu/connlab/machowto/macdecom.html

Installation of downloaded copies:
On all systems, create two folders parallel to each other, one named
shared, and one named explorer, e.g.
  c:\chime\explorer
  c:\chime\shared
Unpack the corresponding self-unzipping EXE file into each folder.
Open explorer\index.htm in Navigator, and bookmark it.

CAUTION: THE FILES IN THE PROTEIN EXPLORER'S SHARED FOLDER ARE NOT YET
COMPATIBLE WITH OLDER RESOURCES SUCH AS THE NONCOVALENT BOND FINDER.
THEREFORE IF YOU HAVE COPIES OF ANY OF MY OTHER CHIME RESOURCES WHICH
INCLUDE A 'SHARED' FOLDER, YOU SHOULD MAKE THE NEW FOLDERS IN A SEPARATE
PART OF YOUR DIRECTORY SYSTEM, KEEPING THE OLD 'SHARED' FOLDER INTACT FOR
WHATEVER IT SERVES.

Enjoy, -Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Protein Explorer: bug fixed
Date: Mon, 05 Oct 1998 09:46:13 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

David Marcey of Kenyon College (author of some of the first and some of the
best Chime tutorials on the web) has already reported a bug in the Protein
Explorer which I offered in beta last evening. I have fixed this bug, which
often prevented loading PDB files.

If you have not tried the Protein Explorer yet, you can skip the next
paragraph.

The bug caused the menu of previously loaded PDB files to become corrupted
by the addition of "(via Internet from the PDB)" to files loaded from the
local disk. Files not loaded previously should appear on the menu correctly
now (after you reload the page with the menu), and after you load 9 new PDB
files, the old corrupted entries will be pushed off the menu list. Browsing
to the file, or typing the 4-character PDB id into the browse slot, should
still work even if the same file is present in corrupted form on the menu.

Thanks, David!

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Alexander Garcia <acad@accefyn.org.co>
Subject: Compiling and Running Raswin
Date: Mon, 05 Oct 1998 16:44:41 -0500
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

Hi there! I am working with windows version of Rasmol (2.5) and I am
trying to change some parts of the code but I have some problems...
I am working with Borland C and first, I made a new projects with all
files, then I compiled it and run it but:
1. The screen display has no the Rasmol Icon and the Rasmol Cursor and
2. The top of this window does not refresh, it is like a Tv with
interference
Could you help me, please? Thanks a lot in advanced!
Leyla Jael.

References: <36193DC9.647566E7@accefyn.org.co>
++++------+------+------+------+------+------+------+------+------+------+
From: Sinasi Ellialtioglu <sinasi@rorqual.cc.metu.edu.tr>
Subject: new in RasMol
Date: Tue, 06 Oct 1998 11:01:20 +0200
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

I have been recently aware of RasMol and been using it for the past couple of weeks
for some simple applications. Not being an expert yet, I undoubdetly have some questions
or need of help, and if you could spare time to reply I would appreciate it very much :

Q1. I will choose an example of N spheres in a a box representing (e.g.) gas molecules.
It is easy to read them in PDB format, and display. However, if I want to annimate the
brownian motion, I will need to reread a new data of N (x,y,z) positions and refresh.
In the Rasmol commands or examples of scripts on the net, I realized that every trick
and skill exist for a defined (or loaded) data of points, but one can not replot or reread
(like in gnuplot for instance). Is there a way to do this, or is there a different program
that you are aware of which can just do that?

Q2. In script writing, is there a way to shorten things like imitating a do loop, or using
variable names like :

n=134
...
select (atomno<=n) and (atomno>n+20)
...?

Q3. Since most literature about Rasmol is dated back to 1995, I am wondering if the status
about certain things has changed already, like :

pause 30
( => wait for 30 sec and go) ?

Thanking you in advance, looking forward to hearing from you
Best Regards

Dr. Sinasi Ellialtioglu
Department of Physics
Middle East Technical University
Ankara, Turkey 06531

++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller  <amuelle3@gwdg.de>
Subject: Re: new in RasMol
Date: Tue, 6 Oct 1998 15:41:24 +0200 (MET DST)
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

On Tue, 6 Oct 1998, Sinasi Ellialtioglu wrote:

Hi for "Real" Animations one can use "Kinemage", but dont't aks me how to
create animations using this program ;-(

> 
> Q2. In script writing, is there a way to shorten things like imitating a do loop, or using
> variable names like :
> 
> n=134
> ...
> select (atomno<=n) and (atomno>n+20)
> ...?
> 

you can use definitions:

define n(134)
select (atomno<=n) and ...

You can keep any rasmol-expression in souch a definition, so
	define special (his, pro, cys)
	define bla( within(3.0, (helix and spcial) and not cys )

or something like this ...
	
> Q3. Since most literature about Rasmol is dated back to 1995, I am wondering if the status
> about certain things has changed already, like :
> 
> pause 30
> ( => wait for 30 sec and go) ?
> 

here's a paragraph of the release.txt of RasMol2.6b2:

[4.2] Pause/Wait Command Potentially one of the most useful additions to
the RasMol command language is the "pause" (synonymously "wait") 
command. This command may be executed in RasMol script files to suspend the
sequential execution of commands and allow the user to examine the current
image. When RasMol executes a "pause" command in a script file, it
suspends execution of the rest of the file, refreshes the image on the
screen and allows the manipulation of the image using the mouse and scroll
bars.  Once a key is pressed, control returns to the script file at the
line following the "pause" command.  While a script is suspended the
molecule may be rotated, translated, scaled, slabbed and picked as normal,
but all menu commands are disabled.  Currently there is no way for the
user to interrupt the execution of a script, for example by typing
control-C or pressing escape, though this may be added in future versions
of RasMol.  The "pause" can probably be used most effectively with "echo"
commands in education pre-scripted demonstrations, where a description of
the current image is presented to the user/student.  Typically the command
before a "pause" should be "echo Press any key to continue".

(you can get the release.txt from: 
ftp://ftp.gwdg.de/pub/misc/rasmol/v2.6beta/ )

Have also a look at:
http://www.umass.edu/microbio/rasmol/distrib/rasman.htm

	good luck,

	Arne

References: <36193DC9.647566E7@accefyn.org.co>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Animations of brownian motion
Date: Tue, 06 Oct 1998 11:03:49 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

At 10/6/98, you wrote:
>I have been recently aware of RasMol and been using it for the past couple
of weeks
>for some simple applications. Not being an expert yet, I undoubdetly have
some questions
>or need of help, and if you could spare time to reply I would appreciate
it very much :
>
>Q1. I will choose an example of N spheres in a a box representing (e.g.)
gas molecules.
>It is easy to read them in PDB format, and display. However, if I want to
annimate the
>brownian motion, I will need to reread a new data of N (x,y,z) positions
and refresh.
>In the Rasmol commands or examples of scripts on the net, I realized that
every trick
>and skill exist for a defined (or loaded) data of points, but one can not
replot or reread
>(like in gnuplot for instance). Is there a way to do this, or is there a
different program
>that you are aware of which can just do that?

I suggest that you do this in Chime 2, for which you will need to work on
Window 95 or NT4 because it is available only for that at present.

You can put the multiple frames either in XYZ or NMR format.  I have no
experience with XYZ but you can see examples of such animation at
www.mdli.com (chime 2 demos) or at
http://www.umass.edu/microbio/chime/anim_xyz/anim.htm

I have been using NMR format and I'm not sure what the pros and cons are
vs. XYZ.  My best example of this is my protein morpher at
http://www.umass.edu/microbio/chime

Contact me if you want a copy which you can explore to see how it is done.
Much of the javascript cannot be obtained easily from the web.

>Q2. In script writing, is there a way to shorten things like imitating a
do loop, or using
>variable names like :
>
>n=134
>...
>select (atomno<=n) and (atomno>n+20)
>...?

Not in RasMol or in Chime directly. This is best done for Chime in
javascript which can then hand the resulting commands to Chime.  This is
how the morpher works.

>Q3. Since most literature about Rasmol is dated back to 1995, I am
wondering if the status
>about certain things has changed already, like :
>
>pause 30
>( => wait for 30 sec and go) ?

RasMol is no longer being developed.  The 'delay N' command (N seconds) is
implemented in Chime which is being developed by MDLI.

I would be very interested in hearing about your progress.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <3619DC60.9A993C1A@rorqual.cc.metu.edu.tr>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: new in RasMol
Date: Tue, 06 Oct 1998 11:12:02 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

At 10/6/98, you wrote:
>On Tue, 6 Oct 1998, Sinasi Ellialtioglu wrote:

[followup to Arne Mueller's reply]

One of the things in my 'morpher' at http://www.umass.edu/microbio/chime
is a display in Chime 2 very much like a kinemage, by the way.

If you want to develop rasmol scripts, be sure to see also my page
"How To Make Your Own Educational BioMolecular
        Structure Presentaions with RasMol or Chime "
at http://www.umass.edu/microbio/rasmol/maketuts.htm

which includes
"Guide to "Movie" Script Creation for RasMol and
Chime" at http://www.umass.edu/microbio/rasmol/makescrp.htm

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <3619DC60.9A993C1A@rorqual.cc.metu.edu.tr>
 <36193DC9.647566E7@accefyn.org.co>
++++------+------+------+------+------+------+------+------+------+------+
From: SKG <skg@asis.com>
Subject: Re: Animations of brownian motion
Date: Tue, 06 Oct 1998 10:53:24 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

>>
>>Q1. I will choose an example of N spheres in a a box representing (e.g.)
>gas molecules.
>>It is easy to read them in PDB format, and display. However, if I want to
>annimate the
>>brownian motion, I will need to reread a new data of N (x,y,z) positions
>and refresh.
>>In the Rasmol commands or examples of scripts on the net, I realized that
>every trick
>>and skill exist for a defined (or loaded) data of points, but one can not
>replot or reread
>>(like in gnuplot for instance). Is there a way to do this, or is there a
>different program
>>that you are aware of which can just do that?
>
One way is to use a program like re_view
http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/
to create multiframe xyz files. The problem is creating an algorithm to
describe the motion
of the molecules. For simple molecular vibration mopac can be used - it's
output files can be read by re-view & translated directly into xyz files.
This can be done with other high end mol modelers like gaussian, spartan,
etc. but re-view is much cheaper (about $100).
And mopac is free - it can calculate reaction intermediates as well as
other states - check it out (the manual is pretty user unfriendly, but play
around with it - it'll work).
Brownian motio is more complex - there may be a modeler that will handle
it. There's several fractal programs that model brownian motion pretty well
also.
 Interesting problem - let us know how you do it  ;*)
- - - - - - - - - - - -
_ _ _ _ _ _ _ _ _

Steven K. Gill

"Against the ruin of the world there is only one defense - the creative
act."  Kenneth Rexroth

References: <3606c516.microb@microb.ffyb.uba.ar>
X-Accept-Language: en
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <a.mueller@icrf.icnet.uk>
Subject: Re: RasMol 2.6 Source Code
Date: Wed, 07 Oct 1998 17:03:15 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

Fernando Gabriel Ranea wrote:
> 
> Dear Rasmolers:
> 
> Where I can obtain the RasWin 2.6 Source Code? I have downloaded a source
> code from GlaxoWellcome Home Page but it is the version 2.4/2.5 for Windows.
> Sincerely,
> 
> Fernando Gabriel Ranea
> fgranea@microb.ffyb.uba.ar

Hi,

try ftp.gwdg.de/pub/misc/rasmol/

or 

ftp ftp.roko.goe.net/pub/rasmol (see also
http://www.roko.goe.net/~amuell4 for a description of RasMol2.6bx1)

	by,
	Arne

-- 
Arne Mueller
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX, U.K.
phone : +44-(0)171 2693405      | Fax : +44-(0)171 269 3258
email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/

++++------+------+------+------+------+------+------+------+------+------+
From: "Bourdon, David M." <BourdonD@health.missouri.edu> (by way of Eric Martz <emartz@microbio.umass.edu>)
Subject: viewing dbl bonds in ball&stick mode
Date: Thu, 08 Oct 1998 13:35:26 -0400
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: BourdonD@health.missouri.edu

I am redirecting this to the list for David Bourdon to circumvent technical
difficulties.
While I'm doing it, I'll point out the discussion of how to show double
bonds at the FAQ,

http://www.umass.edu/microbio/rasmol/faq_em.htm
One statement there is "Beware that if the sticks get too large, the double
bonds will
disappear (reduce the size of your graphics window, or zoom to smaller size)."
-Eric

David's message:

I'm new to RasMol (using v 2.6) an I'm only using it for teaching
purposes at the moment.  The topic of my question has been discussed
previously regarding pdb files but this question is much more
simplistic.  I'm creating a slide to describe the synthetic pathway of
biogenic amines.  Therefore, I use the C4 molecular library
(http://c4.cabrillo.cc.ca.us/projects/library/index.html) to export .mol
files to ISIS/DRAW where the files may be edited and exported to RasMol
in .mol format (although, can I edit a .mol file in RasMol, I'm not
sure?). At this point the wireframe structure clearly displays the
double bonds.  If I choose ball & stick, they disappear.  I'm not sure
if the "set bonds" command pertains to this or not? Thanks for you help.

Kind Regards,

David

David M. Bourdon - Turner Lab
Department of Pharmacology
University of Missouri-Columbia School of Medicine
Columbia, MO 65212 USA
TEL 573-882-1546
FAX 573-884-4558
BourdonD@health.missouri.edu

www.missouri.edu/~c680296

X-MSMail-Priority: Normal
++++------+------+------+------+------+------+------+------+------+------+
From: "Van de Wiele Annie" <avandewiele@nordnet.fr>
Subject: Re: image in script file
Date: Thu, 8 Oct 1998 21:51:19 +0200
To: <rasmol@dhcp-srv2.oit.umass.edu>

Good Morning, 
I' am also interested by  this question.
I' am waiting for the answer.
Thank you to all Rasmol Users.
Annie.
E.mail :avandewiele@nordnet.fr

----------
> De : SKG <skg@asis.com>
> A : rasmol@dhcp-srv2.oit.umass.edu
> Objet : image in script file
> Date : dimanche 4 octobre 1998 20:23
> 
>    Hi all - Could someone please tell me what the trick is to placing
text
> in a rasmol script? For instance, one is writing a tutorial & wants a
title
> page or a pdb file that will create this illusion.
> Thank you kindly.................
> - - - - - - - - - - - -
> _ _ _ _ _ _ _ _ _
> 
> Steven K. Gill
> 
> "Against the ruin of the world there is only one defense - the creative
> act."  Kenneth Rexroth

++++------+------+------+------+------+------+------+------+------+------+
From: Alexander Garcia <acad@accefyn.org.co>
Subject: rasmol
Date: Thu, 08 Oct 1998 15:05:18 -0500
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

Hi there! I am working with the windows version of Rasmol (2.5) and I am

trying to change some parts of the code but I have had some problems...
I am working with Borland C and first, I  developed a new project (*.ide
file) with all
files, then I compiled it and run it but:
1. The display that I got did not have the  Rasmol Icon,  nor  the
Rasmol Cursor
2. The top of this window does not refresh, it is like a Tv with
interference, the menu does not appear (file, edit.....)
Could you help me, please? Thanks a lot in advanced!

PS Please any help I really need it becoese I have done this a lot of
times and always I get the same problem. cheers
Leyla Jael.

++++------+------+------+------+------+------+------+------+------+------+
From: Dan Roseman <drose07@sneezey.bimcore.emory.edu>
Subject: Chime w/scripts
Date: Thu, 8 Oct 1998 18:48:54 -0400 (EDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Hello,

Q:  I find that there are two ways to send commands to Chime.
	1) Through a script that is referred to in the index html
or 	2) commands embedded directly in the index html (or individual
frame's source, etc...)

however, when a script is written out through Rasmol, and then pasted into
the html, AND assuming semi-colons were used appropriatly, there is still
a small problem, that is, when a select command such as "atomno>=186" is
used, the html reads the ">" as an end of a tag!  How do I get around this
and have the html essentially skip over all the >'s in the script and
continue on to the next tag?

I'm trying to do this so I can just pasted the scripts in the html rather
than have 5 or 10 additional files to organize...
thanks.

++++------+------+------+------+------+------+------+------+------+------+
From: lynna@cgl.ucsf.EDU
Subject: Re:  Chime w/scripts
Date: Thu, 8 Oct 1998 16:25:56 -0700 (PDT)
To: rasmol@dhcp-srv2.oit.umass.edu

> 
> Hello,
> 
> Q:  I find that there are two ways to send commands to Chime.
> 	1) Through a script that is referred to in the index html
> or 	2) commands embedded directly in the index html (or individual
> frame's source, etc...)
> 
> however, when a script is written out through Rasmol, and then pasted into
> the html, AND assuming semi-colons were used appropriatly, there is still
> a small problem, that is, when a select command such as "atomno>=186" is
> used, the html reads the ">" as an end of a tag!  How do I get around this
> and have the html essentially skip over all the >'s in the script and
> continue on to the next tag?
> 
> I'm trying to do this so I can just pasted the scripts in the html rather
> than have 5 or 10 additional files to organize...
> thanks.
> 

For  <    type    &le 
     >            &ge
     &            &amp
 copyright        &copy
 registered       &reg
  degree          &deg

You can also check out:

http://www.w3.org/TR/

and look it up.  They have a complete list there, somewhere....

-Aenoch Lynn
 

 mory.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Chime w/scripts
Date: Fri, 09 Oct 1998 09:40:09 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Dan: regarding your > problem, what I do is just leave the RasMol-saved
scripts in a script
disk file (must end in .spt), and then in the html, just call the script,
e.g. 'script file1.spt;'.
For web service, you must set the server's mime table so .spt is served as
application/x-spt so that Netscape hands the script file to Chime.

At 10/8/98, you wrote:
>
>Hello,
>
>Q:  I find that there are two ways to send commands to Chime.
>	1) Through a script that is referred to in the index html
>or 	2) commands embedded directly in the index html (or individual
>frame's source, etc...)
>
>however, when a script is written out through Rasmol, and then pasted into
>the html, AND assuming semi-colons were used appropriatly, there is still
>a small problem, that is, when a select command such as "atomno>=186" is
>used, the html reads the ">" as an end of a tag!  How do I get around this
>and have the html essentially skip over all the >'s in the script and
>continue on to the next tag?
>
>I'm trying to do this so I can just pasted the scripts in the html rather
>than have 5 or 10 additional files to organize...
>thanks.
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Gale Rhodes <rhodes@usm.maine.edu>
Subject: Chime 2
Date: Fri, 9 Oct 1998 10:15:17 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

A colleague of mine, an organic chemist who uses Chime 1 extensively for
small molecule displays in his web pages, suggests that a useful addition
to Chime 2 would be a choice of two menus, a simpler one like Chime 1, and
a full one. It should be possible also for calls to Chime in web pages to
specify which set of menus is the default for that particular display.

For small molecule displays, probably 95% of Chime 2 menu options do not
apply. With the option of Chime 1 menus (or an even simpler set), students
new to this kind of thing would not be confronted with a zillion options,
most of which have no effect.

If you would like to see what he does with Chime, or his other teaching
tools for organic chemistry, see

http://macweb.acs.usm.maine.edu/chemistry/newton/Chy251_253/Topics.html

Cheers!

*****************************

Gale Rhodes   mailto:rhodes@usm.maine.edu
http://macweb.acs.usm.maine.edu/chemistry/GR/GRHomePage.html
Professor of Chemistry
Chemistry Department
University of Southern Maine
PO Box 9300
Portland, Maine 04104-9300
Phone: (207)780-4734 (W)
Fax:   (207)780-5607 (W)

References: <l03020902b243c8f44582@[130.111.128.91]>
++++------+------+------+------+------+------+------+------+------+------+
From: William R Mcclure <wm0p+@andrew.cmu.edu>
Subject: Re: Chime 2
Date: Fri,  9 Oct 1998 11:54:48 -0400 (EDT)
To: rasmol@dhcp-srv2.oit.umass.edu

Excerpts from mail: 9-Oct-98 Chime 2 by Gale Rhodes@usm.maine.ed 
> a useful addition
> to Chime 2 would be a choice of two menus, a simpler one like Chime 1, and
> a full one. It should be possible also for calls to Chime in web pages to
> specify which set of menus is the default for that particular display.

  I agree.
  I made a similar suggestion to Jean holt (MDL) a few weeks ago as part
of my comments on their Mac-beta version of Chime2. For use by CMU
students, the issue comes up in terms of what version of the software
should be installed campus-wide in all of our computer clusters. Since
Chime1 is now being used for simple visualization of molecules by
freshman and sophomore students, installing the full 2.0 version in all
of our clusters would not be a good idea.  However, the new JavaScript
and Live Connect features of 2.0 would enhance the use of 1.0 for all
displays.
  I wonder whether the plugin installation menu could be formatted so
that one has options of e.g. "Easy Install" (you get everything) and
"Choose the Desired Menus". That's similar to a lot of other software
installation pgms.

-Will McClure 

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Mac Chime 2.0b1 observations/bugs
Date: Sat, 10 Oct 1998 11:44:20 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

I've used Chime 2.0b1 a bit on the Mac with Netscape Nav 4.06, and have a 
few issues/bugs I've observed. I'll use the following abbreviations: 
PC/Chime2b4 for PC with Netscape 4.05 and Chime 2.0 beta 4, Mac/Chime1 
for the Macintosh with Netscape 3.04 and Chime 1, and Mac/Chime2b1 for 
Mac with Netscape 4.06 and Chime 2.0 beta 1. Also by "plug-in window" I 
mean the small window that an <embed>ded Chime model appears on on a web 
page, usually with black background.

I use the C4 project's Chime Tutorial 
(http://c4.cabrillo.cc.ca.us/projects/chime_tutorial/) for most of my 
testing.

1. Stick models are too small with Mac/Chime2b1. For example, I am using 
a model that is created by an <embed> in a web page. It is set to sticks 
with display3d=sticks, and set to a certain size using the script command 
zoom. The model's size, and how well it fills out its plug-in window, is 
very consistent between PC/Chime2b4 and Mac/Chime1. However in 
Mac/Chime2b1 the model is about half as big, and therefore it doesn't 
fill out its plugin window at all. It's not entirely consistent, however 
- sometimes if you reload the page the model comes up at the expected 
size.

A work-around may be to use the scripting command "wireframe 40" to 
approximate sticks thickness, instead of using the display3d embed 
option. However it still comes up at the tiny size once in a while.

Spacefilling, wireframe, and ball&stick models all appear to be 
size-consistent with all compared platforms and versions.

2. Using Javascript to open new windows containing Chime models either 
crashes Netscape or doesn't work most of the time. We have links beneath 
each model in the Chime Tutorial that open a new window containing a full 
size version of the model. Most of these will crash the browser every 
time. The one that opens a full-sized model of myoglobin doesn't crash, 
but merely opens an empty window. These all work fine with PC/Chime2b4 
and Mac/Chime1. 

I have not yet tested either of these problems with the combination of 
Mac/Netscape3.04/Chime2.0b1. The older Netscape 3.04 is the only version 
that appears to be completely stable with Chime 1 on the Mac. Chime 1 
with any Netscape 4 version on the Mac will crash reliably any time a 
page is loaded containing multiple Chime models embedded inside tables. 
It is possible that Chime 2 is also more stable with the older NS3.04, so 
I will give that a try.

regards,
Slaton Lipscomb
C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

++++------+------+------+------+------+------+------+------+------+------+
From: "Craig T. Martin" <CMartin@chem.umass.edu>
Subject: Re: RASMOL digest 66
Date: Sun, 11 Oct 1998 09:31:23 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

>Date: Sun, 04 Oct 1998 23:24:04 -0400
>From: Eric Martz <emartz@microbio.umass.edu>
>To: rasmol@dhcp-srv2.oit.umass.edu
>Cc: rhodes@usm.maine.edu, brian.white@umb.edu
>Subject: Protein Explorer beta available
>Message-ID: <0F0C006KQ47D9H@rfd1.oit.umass.edu>
>MIME-version: 1.0
>Content-type: text/plain; charset="us-ascii"
>
>I have made available a beta-test version of a new Chime resource, the
>Protein Explorer, at
>
>http://www.umass.edu/microbio/chime/beta/explorer/index.htm  It is not yet
>publically linked to my Chime site, pending feedback and further testing.
>It is not downloadable from the public location, but is from a private one
>(see below). I would value feedback from anyone interested, especially
>Macintosh users.

Eric -

  A very quick test. It successfully loaded a local PDB file from a
completely different directory structure, so that works fine. The basics
seem to work. But then when I resized the window, I lost the structure
image.

  Also, when I tried to go to another WEB page, it launched a new window.
I've never seen that before. Then when I tried to manually close the
explorer window, Netscape (4.06) crashed altogether. No doubt some
Javascript problem. Despite the goal of Java to be platform independent, I
find that different platforms indeed do implement it differently. This
often causes troubles...

Craig

Craig Martin      ***       Chemistry      ***      X5-3299

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Mac Chime 2.0b1 observations/bugs
Date: Tue, 13 Oct 1998 10:52:12 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

[I am redirecting this message from Will McClure to circumvent technical
difficulties. -Eric]

Excerpts from mail: 10-Oct-98 Mac Chime 2.0b1 observation.. by
slaton@surfnetusa.com 
> 2. Using Javascript to open new windows containing Chime models either 
> crashes Netscape or doesn't work most of the time.

  I couldn't tell what kind of JavaScript you are using from looking at
the "Source" of the methanol tutorial page.  However, I have found that
new windows with images are more reliably served up if JScript is used
to open a separate HTML file.  This approach also lets you do whatever
formatting, color, etc. you want.  An example that works with Nav 4.05
can be seen at:

http://info.bio.cmu.edu/Courses/BiochemMols/nucIDCQz/nucQCMain.htm
  The top frame has a selection form, from which the viewer can choose
from a list of 15 nucleotides. The JScript function and its variables
are all in the HTML of the "nucQCMenu.htm" file.

-Will McClure 
wm0p+@andrew.cmu.edu 

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: "Andrew W. Maverick" <chmave@unix1.sncc.lsu.edu>
Subject: inorganic crystals Chime pages
Date: Wed, 14 Oct 1998 10:57:31 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Dear Chime users,
	It seemed to me that there was a lot of information out there on
biological and organic molecules, but very little on crystals; so I put
together some Chime pages on inorganic crystals for my inorganic chemistry
class to look at.  (Many inorganic structures are available at
http://cst-www.nrl.navy.mil/lattice/
, but in a number of cases Chime does not recognize the atoms as bonded, so
you don't even see the structures in wireframe mode; also, they are not
annotated much.)
	In any case, you can start in
http://www.chem.lsu.edu/lucid/maverick/crystals.htm
and then choose the type of crystal to examine.  Of course each embedded
Chime picture refers to a pdb file for that crystal structure, which you
can download via the Chime menu if you wish.
	I'd appreciate any comments.  Thanks!
	Andy Maverick
Andrew W. Maverick
Department of Chemistry
Louisiana State University
Baton Rouge  LA  70803-1804
USA
Telephone:  (225)388-4415
Fax:  (225)388-3458
E-mail:  chmave@unix1.sncc.lsu.edu
Alternate e-mail:  awm@chem.lsu.edu

++++------+------+------+------+------+------+------+------+------+------+
From: Dan Roseman <drose07@sneezey.bimcore.emory.edu>
Subject: Re:  Chime w/scripts
Date: Thu, 15 Oct 1998 11:08:39 -0400 (EDT)
To: rasmol@dhcp-srv2.oit.umass.edu

	Is it possible to draw lines in a Chime molecule?  I know in Mage
it is possible to add extra lines.  I could, of course, add extra atoms in
the pdb files with connect commands and use those to highlight distances,
but that's not really fun.  I'd like to draw a line from one atom to
another to emphasize a certain distance...

Also, a quick note on the numerical operators:
After every command such as those listed below, a semi-colon must be
inserted.
So,

For    <   type     &lt;	(lt=less than)
for    >            &gt;

the same is true for any other &XXX;

> 
> For  <    type    &le 
>      >            &ge
>      &            &amp
>  copyright        &copy
>  registered       &reg
>   degree          &deg
> 
> You can also check out:
> 
> http://www.w3.org/TR/
> 
> and look it up.  They have a complete list there, somewhere....
> 
> -Aenoch Lynn
>  
> 

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Re:  Chime w/scripts
Date: Thu, 15 Oct 1998 10:11:42 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

On 10/15/98 7:08 AM Dan Roseman wrote:

>Is it possible to draw lines in a Chime molecule?  I know in Mage
>it is possible to add extra lines.  I could, of course, add extra atoms in
>the pdb files with connect commands and use those to highlight distances,
>but that's not really fun.  I'd like to draw a line from one atom to
>another to emphasize a certain distance...

You can draw distance monitor lines between any two atoms in a molecule. 
These are dashed lines, like the default hydrogen bond representation, 
that can either display either the distance in angstroms between the two 
atoms, or nothing at all. They can also be set to whatever color you like.

The syntax is:

monitor atom1 atom2     (to turn on the monitor line)
set monitors [on | off]     (turns on/off the distance display)
monitors off     (to turn off the monitor line)
color monitors mycolor     (to change the color of the line)

Where: 

atom1 and atom2 are atom serial numbers in the pdb file
mycolor is the name of a rasmol color or a decimal [r,g,b] color where r, 
g, and b are between 0 and 255.

regards

C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Re: Mac Chime 2.0b1 observations/bugs
Date: Thu, 15 Oct 1998 10:25:53 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

On 10/13/98 6:52 AM Will McClure wrote:

>Excerpts from mail: 10-Oct-98 Mac Chime 2.0b1 observation.. by
>slaton@surfnetusa.com 
>> 2. Using Javascript to open new windows containing Chime models either 
>> crashes Netscape or doesn't work most of the time.
>
>  I couldn't tell what kind of JavaScript you are using from looking at
>the "Source" of the methanol tutorial page.  However, I have found that
>new windows with images are more reliably served up if JScript is used
>to open a separate HTML file.  This approach also lets you do whatever
>formatting, color, etc. you want.  An example that works with Nav 4.05
>can be seen at:
>http://info.bio.cmu.edu/Courses/BiochemMols/nucIDCQz/nucQCMain.htm

In the example I mentioned, we have an invisible script pane in the 
frameset (the joys of Chime 1, before the days of LiveConnect). The 
frameset contains a Javascript function that pops open the new window and 
then dynamically writes an html page to it, containing a Chime plug-in of 
the clicked-on molecule with our preferred colors, rendering, any 
scripts, etc. So in a sense, yes we are using Javascript to open a new 
html file, although this is a dynamic one rather than an actual physical 
.html file. 

So the problem with Chime2b1/Mac involves Javascript. Lazar Mizrakhi of 
MDLI contacted me after that post and they have observed the crash & are 
working on a solution. Not sure yet if this is for sure a problem with 
Chime or if something in our Javascript is funky (although it works fine 
with all other Chime releases). It was written quite some time ago, so 
that is certainly possible.

regards,
Slaton Lipscomb

C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: New PDB
Date: Tue, 20 Oct 1998 13:56:18 -0400
To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu

I just learned of the URL for the new PDB.  As a result of the recent
funding competition, the Research Collaboratory for Structural
Bioinformatics is scheduled to take over the PDB in October, 1999.  At
their website, http://www.rcsb.org/ you can find a press release dated
10/1/98, FAQ about transition and management, and the successful grant
proposal. The existing PDB has also made their grant application available
(www.pdb.bnl.gov).

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: kt200993@regiscollege.edu
Subject: running a script in twoframe
Date: Wed, 28 Oct 1998 10:30:15 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

I am learning how to use RASMOL, and I am trying to run a
"movie" script in the twoframe program to see the progress.  I
have read the instructions many times over, and this is what I
am doing.  I write the script in wordpad.  Then I open twoframe.
 The directions then say to open the wordpad file from the
twoframe, but it is looking for an internet site, not something
on a disk.  The directions also say that reload is supposed to
work, but this just reloads the blank twoframe page.  Does
anyone know how to make the script come up in the twoframe
program to view the movie with the appropriate buttons?  

        jsr@kinemage.biochem.duke.edu, dcr@kinemage.biochem.duke.edu
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: demonstating crystal contacts in PC freeware
Date: Thu, 29 Oct 1998 01:08:48 -0500
To: pdb-l@pdb.pdb.bnl.gov, rasmol@dhcp-srv2.oit.umass.edu
Cc: fleming@csb.yale.edu, thompson@chem.umass.edu, cmartin@chem.umass.edu,

I am teaching (for the first time) a class in macromolecular visualization
(not modeling). (The class website is
http://bcrc.bio.umass.edu/courses/fall98/micbio/micbio797v/) The class is
based largely on RasMol and Chime.

I want to be able to show crystal contacts with freeware which runs on
PC's.  I would appreciate advice on how most easily to do this. Perhaps
there are tutorials or examples already illustrated on the web? I would
also like suggestions for good examples, including a case where crystal
contacts affect structure.

The only case I'm aware of is the one mentioned in Gale Rhodes book
"Crystallography made crystal clear", where on page 34 he mentions that a
loop in one molecule of the pair for malate dehydrogenase (4mdh I assume)
is affected by crystal contacts. Perhaps there is a more dramatic case?

So far, I am trying to generate the contacts with Swiss PDB Viewer by
Nicolas Guex. With it you can fill out the unit cell relatively easily, but
translations must then be done manually (as far as I can see) to make sure
you represent all the molecules in contact with a central molecule. If
anyone has experience on how most easily to use Swiss PDB Viewer to do this
please let me know.

If it would be much easier, I can use commercial software (which is best?)
to generate the PDB file containing contacts, then display/analyze the
contacts in freeware (e.g. my Noncovalent Bond Finder implemented in Chime,
http://www.umass.edu/microbio/chime/find-ncb/index.htm).

-Eric Martz
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: Windows/Chime & RasMol
Date: Sun, 01 Nov 1998 13:03:05 +0200
To: RasMol list <rasmol@dhcp-srv2.oit.umass.edu>

I've been playing around with Netscape 4.07 on Windows 95, trying to use
both Chime (for the MIME type chemical/x-pdb) and RasMol (for the MIME
type application/x-rasmol).
I'm not such an expert with Windows, so maybe someone can help out.

Chime 1.0 is fine to use with RasMol, but as soon as I install Chime
2.0b3 it inserts the instruction to open application/x-rasmol with
Chime.

The only way around this I know is to disable Chime (by putting it a new
folder called something like 'Plugins (disabled)' and restarting
Netscape), but this is a hassle every time you want to change browsers.

Has anyone else found a trick of either how to install Chime 2 without
enabling some of the pre-set MIME types. Or how to modify the MIME type
in Preferences|Applications (the Edit and Remove buttons cannot be
selected).

Thanks,
Kurt

-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +972-8-9342614
Weizmann Institute of Science   Fax: +972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: "Brian White" <brian.white@umb.edu>
Subject: Which version of netscape is best?
Date: Wed, 04 Nov 1998 10:59:42 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Hi
    I'm running netscape 4.06 on power mac g3 all-in-ones with chime 2.0
beta & it's a little flaky sometimes - strange intermittent problems
that are usually solved by a netscape re-load, but confusing to my intro
students. Any suggestions as to which version of netscape is the most
stable on the mac with javascript & chime 2.0 beta?

Brian

        rhodes@usm.maine.edu, cmartin@chem.umass.edu
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Chime 2 is released!
Date: Tue, 03 Nov 1998 23:42:20 -0500
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: jls@bnl.gov, lsprilus@inherit1.weizmann.ac.il, wm0p@andrew.cmu.edu,

MDL released Chime 2 (full release, not beta!) for Windows and Macintosh
(!!) yesterday. Get it from http://www.mdli.com/download/chime2.html

I have no info yet on how well the Macintosh version works but please let
me know, you Mac users. I'm especially interested in whether my protein
morpher and noncovalent bond finder will work as is with the Mac version.
If there are problems with version detection, go directly to 

Finder:

http://www.umass.edu/microbio/chime/find-ncb/fs_tutm3.htm

Morpher:

http://www.umass.edu/microbio/chime/morpher/fs_mtop.htm

Don't use these URL's unless it refuses to recognize the new Chime 2 version.
Try the regular route first, namely

http://www.umass.edu/microbio/chime/index.html

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

        <brian.white@umb.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Re: Which version of netscape is best? (for Mac)
Date: Wed, 4 Nov 1998 08:51:29 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>,

On 11/4/98 7:59 AM Brian White wrote:

>    I'm running netscape 4.06 on power mac g3 all-in-ones with chime 2.0
>beta & it's a little flaky sometimes - strange intermittent problems
>that are usually solved by a netscape re-load, but confusing to my intro
>students. Any suggestions as to which version of netscape is the most
>stable on the mac with javascript & chime 2.0 beta?

Unfortunately they're all at least a little flaky. Probably the safest 
Netscape for any version of Chime on the Mac is 3.04. There you will 
still have occasional problems with models appearing in the upper-left 
corner of the screen instead of where they are supposed to be on a web 
page, but overall it is a reliable, stable combination. Unfortunately 
this version of Netscape has some memory management issues and so it must 
be quit and restarted after a half hour or so of using Chime to prevent 
it from crashing. 

Chime 1 and Netscape 4.0x on the Mac don't work well at all with multiple 
models embedded in tables (invisible or not). Too many of these will 
crash the browser every time.

Chime 2b1 and Netscape 4.0x can handle the models-in-tables issue, but 
have a few new problems aside from that, as you have discovered. Sticks 
models don't come up zoomed as large as they should, and using certain 
Javascript code in conjunction with Chime crashes the browser. MDLI is 
looking into this.

regards,
Slaton Lipscomb
C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

++++------+------+------+------+------+------+------+------+------+------+
From: Clifford Felder <cffelder@weizmann.weizmann.ac.il>
Subject: Does Chime 2 for MacIntosch work with Netscape 4.5 for Mac?
Date: Thu, 05 Nov 1998 09:16:37 +0200
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: joel@sgjs3.weizmann.ac.il

Dear Eric Martz and the Rasmol-Chime list,
  Does the new Chemscape Chime 2 (Netscape/IE) Plugin for MacIntosch
work with the recently-released Netscape version 4.5 for MacIntosch? How
well does it work compared with previous versions of Netscape? Thank you
for sharing your experience with the list members.
Sincerely, Clifford Felder <cffelder@weizmann.weizmann.ac.il>
Dept. of Structural Biology, Weizmann Institute, Rehovot Israel

        emartz@microbio.umass.edu
++++------+------+------+------+------+------+------+------+------+------+
From: Steven Verhey <verhey@elwha.evergreen.edu>
Subject: Re: Does Chime 2 for MacIntosch work with Netscape 4.5 for Mac?
Date: Thu, 5 Nov 1998 09:05:26 -0800 (PST)
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: rasmol@dhcp-srv2.oit.umass.edu, joel@sgjs3.weizmann.ac.il,

I've been using Chime 2 since the morning I got Eric's alert 
(admittedly, not all that long ago), and it seems to work fine with 
Netscape 4.5.  With 2b I had been noticing various sorts of strangeness, 
which had seemed to be declining in frequency the longer I used 2b.  In 
any event, 2.0 seems to work great, and I'm just beginning to explore 
the new functionalities.

BTW, Eric, I've looked at the Protein Morpher just briefly.  The Morpher 
detects my netscape/chime versions fine and lets me in, but when I try to 
look at calmodulin/apo flexibility or calmodulin/effect of binding 
calcium, I get a javascript error.  Likewise recoverin/14 steps. I can 
try to give more details if it will help.

Steve Verhey 
The Evergreen State College  

On Thu, 5 Nov 1998, Clifford Felder wrote:

> Dear Eric Martz and the Rasmol-Chime list,
>   Does the new Chemscape Chime 2 (Netscape/IE) Plugin for MacIntosch
> work with the recently-released Netscape version 4.5 for MacIntosch? How
> well does it work compared with previous versions of Netscape? Thank you
> for sharing your experience with the list members.
> Sincerely, Clifford Felder <cffelder@weizmann.weizmann.ac.il>
> Dept. of Structural Biology, Weizmann Institute, Rehovot Israel
> 

++++------+------+------+------+------+------+------+------+------+------+
From: Julia Yu <Juliay@mdli.com>
Subject: Chime 2 is available
Date: Fri, 6 Nov 1998 10:20:00 -0800 
To: "'rasmol@dhcp-srv2.oit.umass.edu'" <rasmol@dhcp-srv2.oit.umass.edu>
Cc: Jean Holt <jch@mdli.com>

Chime 2.0 is now available for Windows 95, Windows NT 4.0 and Macintosh
PowerPC.  This major release has many enhancements which include:

    * Compatibility with Netscape Communicator (3.04, 4.05 and later)
    * Compatibility with Internet Explorer 4.01 (Windows 95 and NT)
    * Enhanced 2D rendering including the ability to display TGF files, 
      Sketch files (platform specific), RGroups, and Polymers
    * Support for Gaussian Cube files
    * Support for Rasmol Script files
    * Support for Log P calculations
    * Support for Color Amino Acids
    * Rendering of ISIS 3D query feature display in the 3D layer
    * Programmatic access from either JavaScript or Java via   
      LiveConnect (Netscape only)
    * Ability to copy a Chime script to the clipboard
    * Ability to generate and display molecular surfaces
    * Ability to calculate charges on atoms
    * Support for Sprout Hydrogens
    * Integrated Sculpt visualization and direct link to Interactive 
      Simulations' Sculpt visualization application
    * JCAMP-DX reader and viewer using code licensed from the University 
      of West Indies, Mona Jamaica (Windows 95 and NT)
    * Hot link to ISIS/Draw (version 2.1.4 and later) via double click  
      in 2D mode for mol, rxn, tgf and skc file types
    * Expanded Chime scripting capabilities. Please see the Chime FAQ on
      MDL's Web site for details
    * Chime mouse help menu for displaying Chime's mouse control 
      commands (Mouse/Open Mouse Control Help Page)

Chime software and documentation are delivered via the MDL Information 
Systems, Inc. (MDL) web site.  To access the products, installation 
instructions, and technical materials, please use your web browser to 
connect to one of the following URLs:

  http://www.mdli.com/download 
  http://www-uk.mdli.com/download

Read the instructions on the web pages to download and install your 
software.  Please check the MDL web site regularly since release 
notes, documentation and future updates of Chime will be delivered 
from that location.  

Thank you again for choosing Chime as your Intranet and Internet 
visualization tool.

Sincerely,

The Chime Team
MDL Information Systems, Inc.

++++------+------+------+------+------+------+------+------+------+------+
From: TIMOTHY DRISCOLL <tdriscol@unix.amherst.edu>
Subject: Chime 2.0 for the Mac problems
Date: Fri, 6 Nov 1998 14:57:48 -0500 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu

Rasmol list members,

I know it has only been available for a few days, but I'm having trouble
with Chime 2.0 on my Mac and I wonder if anyone can help.  I'm using
Netscape 4.05, and I can pull up a Chime window, but no structure is
loaded.  Even using a very simple html file containing just the EMBED
command, I still can't view it.  Chime 1.0 works just fine, though.

Any ideas?

Tim Driscoll

++++------+------+------+------+------+------+------+------+------+------+
From: Franklin Adler <Franklina@mdli.com>
Subject: RE: Chime 2 is available
Date: Fri, 6 Nov 1998 12:06:24 -0800 
To: "'rasmol@lists.umass.edu'" <rasmol@dhcp-srv2.oit.umass.edu>

Thank you for sending the letter to the rasmol list.

> -----Original Message-----
> From:	Julia Yu [SMTP:Juliay@mdli.com]
> Sent:	Friday, November 06, 1998 10:20 AM
> To:	'rasmol@dhcp-srv2.oit.umass.edu'
> Cc:	Jean Holt
> Subject:	Chime 2 is available
> 
> Chime 2.0 is now available for Windows 95, Windows NT 4.0 and Macintosh
> PowerPC.  This major release has many enhancements which include:
> 
>     * Compatibility with Netscape Communicator (3.04, 4.05 and later)
>     * Compatibility with Internet Explorer 4.01 (Windows 95 and NT)
>     * Enhanced 2D rendering including the ability to display TGF files, 
>       Sketch files (platform specific), RGroups, and Polymers
>     * Support for Gaussian Cube files
>     * Support for Rasmol Script files
>     * Support for Log P calculations
>     * Support for Color Amino Acids
>     * Rendering of ISIS 3D query feature display in the 3D layer
>     * Programmatic access from either JavaScript or Java via   
>       LiveConnect (Netscape only)
>     * Ability to copy a Chime script to the clipboard
>     * Ability to generate and display molecular surfaces
>     * Ability to calculate charges on atoms
>     * Support for Sprout Hydrogens
>     * Integrated Sculpt visualization and direct link to Interactive 
>       Simulations' Sculpt visualization application
>     * JCAMP-DX reader and viewer using code licensed from the University 
>       of West Indies, Mona Jamaica (Windows 95 and NT)
>     * Hot link to ISIS/Draw (version 2.1.4 and later) via double click  
>       in 2D mode for mol, rxn, tgf and skc file types
>     * Expanded Chime scripting capabilities. Please see the Chime FAQ on
>       MDL's Web site for details
>     * Chime mouse help menu for displaying Chime's mouse control 
>       commands (Mouse/Open Mouse Control Help Page)
> 
> Chime software and documentation are delivered via the MDL Information 
> Systems, Inc. (MDL) web site.  To access the products, installation 
> instructions, and technical materials, please use your web browser to 
> connect to one of the following URLs:
> 
>   http://www.mdli.com/download 
>   http://www-uk.mdli.com/download
> 
> Read the instructions on the web pages to download and install your 
> software.  Please check the MDL web site regularly since release 
> notes, documentation and future updates of Chime will be delivered 
> from that location.  
> 
> Thank you again for choosing Chime as your Intranet and Internet 
> visualization tool.
> 
> Sincerely,
> 
> The Chime Team
> MDL Information Systems, Inc.
> 

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Re: Chime 2.0 for the Mac problems
Date: Fri, 6 Nov 1998 22:56:49 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

On 11/6/98 11:57 AM TIMOTHY DRISCOLL wrote:

>I know it has only been available for a few days, but I'm having trouble
>with Chime 2.0 on my Mac and I wonder if anyone can help.  I'm using
>Netscape 4.05, and I can pull up a Chime window, but no structure is
>loaded.  Even using a very simple html file containing just the EMBED
>command, I still can't view it.  Chime 1.0 works just fine, though.

According to the Readme, Chime 2.0 adds support for several new filetypes 
using already supported mime types. For example chemical/x-pdb supports 
.emb and .embl in addition to .pdb files now. Netscape/Mac is unable to 
automatically update its registry for already existing mime types. The 
Readme instructs you to open Netscape preferences and manually delete the 
registry entries (under "Preferences->Applications" in 4.0x) for all 
supported mime types. Then quit Netscape. The next time you run it, 
Netscape will automatically rebuild the registry entries for the removed 
mime types, and include the newly supported extensions.

Why should NOT doing this prevent you from viewing already supported 
extensions such as .pdb or .mol? Good question. But that's exactly what 
happened to me until I rebuilt the registry as suggested, and now good 
ol' pdb files and molfiles view fine. So that will probably clear up your 
problem.

On a more frustrating note, I am finding that my problems with Chime 
2.0b1 on Mac are still present with Chime 2.0 final. 

That is: sticks models still come up too small by default (compared to 
the identical scripting on Chime 2/Win95 or Chime 1/Mac/SGI/Win95). 

Also, some Javascript we use to spawn new browser windows containing 
Chime models crash Netscape 4.06 every time. This is done with 
dynamically written html in an invisible script pane, rather than with 
LiveConnect in order to maintain Chime 1 compatibility. 

The crashing problem is still present in the Chime 2 final release. 
Perhaps this Javascript - which admittedly we wrote quite a long time ago 
and have reused dozens of time without even looking at it - is sloppy in 
some way, so I guess I will play around with it a bit. Incidentally for 
this crash Macsbug reports an unmapped memory exception, the offending 
call (I assume) being CPluginView::HandleEmbedEvent(CL_Event*).

Don't mean to sound like a complainer - I'm very happy to see Chime 2 out 
of beta and with full LiveConnect support on the Mac. Good job to the 
MDLI team, and thanks.

regards,
Slaton Lipscomb
C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

References: <8E13FBBA26A9DA119ED400A0C9AB2CE55C98D1@shepherd.mdli.com>
++++------+------+------+------+------+------+------+------+------+------+
From: William R Mcclure <wm0p+@andrew.cmu.edu>
Subject: Re: Chime 2 is available
Date: Sat,  7 Nov 1998 09:07:59 -0500 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu

Chime 2ers,

  Has anyone else found that rotation from a "move" script command is
extremely slow?  In contrast, "Rotation" from the Chime menu functions
as expected.
  I use a PowerMacG3, system 8.1, Navigator 4.05.
  This was not my experience with the v2.0 (beta1 for the Mac) on the
same set-up only a few weeks ago.

-Will McClure 

X-Operating-System: Debian/GNU Linux 2.0
++++------+------+------+------+------+------+------+------+------+------+
From: "K. Arun"  <kar@giasmda.vsnl.net.in>
Subject: Re: Chime 2 is available
Date: Sat, 7 Nov 1998 13:02:29 +0530
To: rasmol@dhcp-srv2.oit.umass.edu

On Fri, Nov 06, 1998 at 10:20:00AM -0800, Julia Yu said:

 => Chime 2.0 is now available for Windows 95, Windows NT 4.0 and Macintosh
 => PowerPC.  This major release has many enhancements which include:

Hi,
	I do apologise if this is an FAQ, but is Chime (any version)
available on the Linux/UNIX platform for Netscape
Navigator/Communicator. If not, are there any plans for a port ?

	Thanks.
							- K. Arun

		     -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
K. Arun                             |	                   PGP key particulars
kar@giasmda.vsnl.net.in             |                         Key Id: 5606B2B1
http://aroon.home.ml.org            |                Key: $WWWHOME/pgpkey.html
		     -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

++++------+------+------+------+------+------+------+------+------+------+
From: Jens Grabenstein <Jens.Grabenstein@konstanz.netsurf.de>
Subject: Re: Chime 2 is available
Date: Sun, 8 Nov 1998 09:40:02 +0100
To: <rasmol@dhcp-srv2.oit.umass.edu>, <rasmol@dhcp-srv2.oit.umass.edu>

>Chime 2ers,
>
>  Has anyone else found that rotation from a "move" script command is
>extremely slow?  In contrast, "Rotation" from the Chime menu functions
>as expected.
>  I use a PowerMacG3, system 8.1, Navigator 4.05.
>  This was not my experience with the v2.0 (beta1 for the Mac) on the
>same set-up only a few weeks ago.
>
>-Will McClure 
>
Hello,

it is the same with me. Everything goes extremely slow since I upgraded 
to Chime 2. I also encountered problems with the delay-command. Delays 
take much longer than before. Everything works fine in Chime 1, and there 
is no problem using the same scripts and Chime 2 on a Windows-PC. Does 
anyone know the reason?

Jens

++++------+------+------+------+------+------+------+------+------+------+
From: Frieda Reichsman <friedar@biochem.umass.edu>
Subject: Chime 2 slow move bug
Date: Sun, 8 Nov 1998 11:53:32 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

I am also using a Mac G3 and have experienced the slow "move" and "delay"
command responses in Chime 2.0 using scripts that work fine in Chime 2
beta, so I suspect it is a problem with Chime 2.0 - But has anyone yet
checked this out who is not using a G3?

Frieda

_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Frieda Reichsman, Ph.D.                       _/_/_/_/_/
Biochemistry and Molecular Biology            _/_/_/_/_/
University of Massachusetts                   _/_/_/_/_/
Amherst, MA 01003                             _/_/_/_/_/
email: friedar@biochem.umass.edu              _/_/_/_/_/
Phone: (413) 545-4029                         _/_/_/_/_/
Fax:   (413) 545-3291                         _/_/_/_/_/
Voice mail: (413) 545-4025                    _/_/_/_/_/
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Chime 2 is available
Date: Sun, 08 Nov 1998 00:40:29 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

At 11/7/98, you wrote:
>Hi,
>	I do apologise if this is an FAQ, but is Chime (any version)
>available on the Linux/UNIX platform for Netscape
>Navigator/Communicator. If not, are there any plans for a port ?
>
>	Thanks.
>							- K. Arun

Regrettably, the answers (from MDLI) are NO and NO.
Were they to support any unix platform, it would probably be SGI.  There
are large numbers of potential users in crystallographic research groups
who have only SGI's, no PC's nor Macs. MDLI is quite aware of this but even
their resources are limited and they have announced both here and on their
Chime 2 website that there are no plans for porting Chime 1 or 2 to SGI or
linux, etc.

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: lynna@cgl.ucsf.EDU
Subject: multi-structure nmr files
Date: Sun, 8 Nov 1998 10:41:03 -0800 (PST)
To: rasmol@dhcp-srv2.oit.umass.edu

Chime 2 has the capability to display multi-structure nmr files with all 
the structures overlapped.  The pull-down menu in Chime allows the user
to specify which model(s) he wants to view.  How do I do this from a 
script or an embed tag?  I want to have a series of buttons that change
the display to show only one model at a time.

Thanks for the help.

-Aenoch Lynn
lynna@cgl.ucsf.edu

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: multi-structure nmr files
Date: Sun, 08 Nov 1998 02:42:18 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

At 11/8/98, you wrote:
>
>Chime 2 has the capability to display multi-structure nmr files with all 
>the structures overlapped.  The pull-down menu in Chime allows the user
>to specify which model(s) he wants to view.  How do I do this from a 
>script or an embed tag?  I want to have a series of buttons that change
>the display to show only one model at a time.
>
>Thanks for the help.
>
>-Aenoch Lynn
>lynna@cgl.ucsf.edu
>

At my suggestion, Tim Maffett of MDLI kindly modified Chime 2 so that it
now auto-detects when a PDB file is a multiple-model NMR file (based on the
first MODEL record in the PDB file).  So it is no longer necessary to
include "nmrpdb=1" in the <embed..> which invokes Chime, nor to use 'load
nmrpdb file.pdb' to load the file. (Chime 1 did not handle NMR files even
when these nmrpdb instructions were provided.)

Chime 2 obeys the RasMol syntax for selecting models, e.g. to select model 11,
select ::11
or
select model=11
(Admittedly this is tricky to find in the RasMol Reference Manual
http://www.umass.edu/microbio/rasmol/distrib/rasman.htm
since it is mentioned only under the Label command! However if you search
for 'nmr' you find it easily enough.)

The model=N can be combined with other expressions as complex as you wish,
e.g.
restrict model=11 and not water

To display all models overlaid (as the initial display now does), just
select all, e.g.
select all
wireframe off
backbone

There are buttons to control NMR model displays in the beta test version of
my Protein Explorer/Comparator
(http://www.umass.edu/microbio/chime/beta/explorer/). Here I have also
implemented a form box into which you can type a script which will be the
representation of any model you select from the Model button/form slot.
Thus, as its name implies, this interface works well for general
exploration of PDB files including NMR files, and especially for
side-by-side comparison of two files (in the Comparator) either or both of
which can be NMR files.

The Explorer/Comparator has not yet been upgraded to take full advantage
and cognizance of all the many improvement in the full release of Chime 2
but it works fine as is (just ignore some of the obsolete messages).  I'm
working on a much-improved version.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Jens Grabenstein <Jens.Grabenstein@konstanz.netsurf.de>
Subject: Re: Chime 2 slow move bug
Date: Sun, 8 Nov 1998 20:59:43 +0100
To: <rasmol@dhcp-srv2.oit.umass.edu>, <rasmol@dhcp-srv2.oit.umass.edu>

>I am also using a Mac G3 and have experienced the slow "move" and "delay"
>command responses in Chime 2.0 using scripts that work fine in Chime 2
>beta, so I suspect it is a problem with Chime 2.0 - But has anyone yet
>checked this out who is not using a G3?
>
>Frieda

I am using a PowerMac 7600 with a 604-processor. And it is terriblely 
slow. It just worked fine with Chime 1.

Jens

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: New capabilities in Chime 2 not yet documented by MDL
Date: Sun, 08 Nov 1998 07:12:48 -0500
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: FranklinA@mdli.com, tim@mind.net, jch@mdli.com

The Chime team at MDL, notably Franklin Adler and Tim Maffett, were kind
enough to implement a number of features into Chime 2 at my request. I am
very grateful! Since these may not be documented at the MDL website for
some time, I am summarizing them here. I would also like to thank them for
heroic efforts at fixing bugs, even those reported very late prior to the
scheduled November 3 release.

Before getting to the new features, let me remind you that several quite
powerful features in Chime 1 have never yet been documented at MDL's site
(http://www.mdli.com/download/ch2doc.html), such as the entirely new move,
delay, loop, view, set zoom center commands, and enhancements to the load,
script, slab, and translate commands. Most of these have been documented at
my site for a long time under the link
"Chime 0.99 Partial Draft Manual"

http://www.umass.edu/microbio/chime/manual/chimeman.htm
Many other new capabilities are explained at MDL's site (above) which you
should explore carefully!

The new capability of DISPLAYING MULTIPLE MODELS FROM NMR PDB FILES was
detailed in my message immediately preceding this one, so will not be
repeated below.

Another item reported to this list previously by Tim enables an ARBITRARY
BOND TO BE SHOWN (such as a hydrogen bond) as a regular bond element; this
is also omitted below. (Search for 'set connect save' in the email history
for August '98,
ftp://marlin.bio.umass.edu/pub/shareware/rasmol/email-history/).

Also reported to the list by Tim in May '98 is the 'set zoom center
true|false' capability.

Some commands related to surfaces, MEP coloring, and Chime's new capability
to 'sprout' hydrogen atoms, not yet documented by MDL, were mentioned by
Tim in a June email (search for 'set kollman sprout').

A few MENU capabilities new in Chime 2 are noteworthy:

-Mouse, Open Mouse Control Help Page shows the Shift/Ctrl etc options for
mouse operations, both for Windows and Mac.

-The amino acid color scheme, always available with the 'color amino'
command, is now on the Color menu.

-Options, Sprout hydrogens works but unfortunately they seem not to be
saved in the PDB file with File, Save molecule as.  Lucky guess/good
design: the command 'SPROUT HYDROGEN' exists! (Note: only the singular is
recognized; 'sprout hydrogens' fails, while both 'select hydrogens' and
'select hydrogen' succeed.)

-Select, Display list, perhaps not obviously, can create and color
SURFACES.  Note that there are a variety of options for selecting the probe
radius, and equations used for color schemes, all documented by MDL.

-Select, Residue has an important capability. All 20 amino acids are ALWAYS
listed, but those not present in the structure loaded are grayed out!
Residues other than the 20 standard AA's are shown in a separate list,
making them easy to spot.

-Select, Mouse Click Action allows atoms, residues, and chains to be
selected/deselected as a mouse click toggle!

The new capabilities documented below are:

1. SYNCHRONING MOUSE MOVEMENTS BETWEEN CHIMES
2. RECOGNIZING HEXADECIMAL RGB COLOR VALUES
3. REPORTING NMR MODEL COUNT
4. MESSAGE ORDER SCRAMBLING WORKAROUND

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - -

1. SYNCHRONING MOUSE MOVEMENTS BETWEEN CHIMES

At my suggestion, Tim Maffett implemented this amazing feature:

"I have added an embed tag argument, "sendmouseevents" (or "sendmouse"),
which can be set to true. If this is true then the mouse events of the
chime will be sent to the chime plugin specified in the target='' tag.
example:"

<embed name=chime1 src="connect_test.pdb" width=30% height=70% 
initscript="set connect save" target=chime2 sendmouse=true> 
<embed name=chime2 src="connect_test.pdb" width=30% height=70% 
initscript="set connect false" target=chime3 sendmouse=true> 
<embed name=chime3 src="connect_test.pdb" width=30% height=70% 

target=chime1 sendmouse=true>

"NOTE: each plugin points to the next one, and then the last one (chime3) 
points back to the chime1 plugin. By doing this you can link 2 or more 
plugins mouse movements."

Typically, one needs to align two molecules without sync before enabling
synch.  Therefore, Tim also added the command 'send mouse on|off' (where
'on|off' means the paramater can be either on or off).  It is also possible
to start with the embed tag option 'sendmouse=false' plus a target, then
use the script command 'send mouse on' when you are ready, for example on a
button labeled 'Synchronize mouse movements'.

This mechanism syncrhonizes all mouse-initiated movements, namely x,y,z
rotations, translations, and slab plane movements. It does nothing with
script-initiated movements (by design).

2. RECOGNIZING HEXADECIMAL RGB COLOR VALUES

Chime (a la RasMol) recognizes only decimal rgb colors of the format
[255,255,255], while Navigator recognizes only hexidecimal rgb colors of
the format #FFFFFF. In well-designed Chime presentations, the text near
Chime is colored to provide a key to the colors in the graphic. Matching
the decimal and hex values is a constant nuisance. Therefore Tim added to
Chime the ability to recognize hex RGB colors in this format:

color [x00ff00]

('#' could not be used because this is a chime/rasmol comment character.)

3. REPORTING NMR MODEL COUNT

The old command 'show info' now includes the number of models for NMR files.

Number of Models ...... 24
Number of Turns ..... 0
Number of Strands ... 0
Number of Helices ... 12
Number of Bonds ..... 74094
Number of Atoms ..... 72288 (1056)
Number of Groups .... 4488 (72)
Number of Chains .... 48
Brookhaven Code ..... 1JSA
Secondary Structure . PDB Data Records
Classification ...... CALCIUM BINDING
Molecule name ....... RECOVERIN;

4. MESSAGE ORDER SCRAMBLING WORKAROUND

In order for javascript to know such things as atom counts selected by
select-commands, etc., it is necessary to know which messages arrived after
other messages.  This is made difficult due to a message order scrambling
bug. When a long script is sent to Chime, at first, messages are returned
in order.  But at some point (about when the image appears), the last
message comes out of order, followed by next to last etc. in REVERSE order
until the message just after the discontinuity occurred.  Tim Maffett has
provided the following mechanism to allow message order to be determined:

"The message order scrambling bug is caused by Netscape when a request for
a subsequent file (from a script) is executed, all of the message callbacks
somehow get reversed.... I tried a variety of things to try and work around
this bug, but my 'solution' is to add an addition (*optional*) integer
argument, 'lineNumber' to the message callback:"

function MyMessageCallback( buttonname, message, lineNumber ) 
{ 
	// add this message to our message textarea.... 
	document.theform.chimemessages.value += "" + lineNumber + " : " + 
		message + "\r\n"; 
}

If you know of anything I don't know about, please inform the list!
-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
UMass Chime Site <www.umass.edu/microbio/chime>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

 SGI.
++++------+------+------+------+------+------+------+------+------+------+
From: Gale Rhodes <rhodes@usm.maine.edu>
Subject: Excellent, free Mac and PC modeling program soon available for
Date: Sun, 8 Nov 1998 19:26:30 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

While Chime is not under development for Unix, SwissPdbViewer (SPV) will
soon be available in a prerelease version for SGI. It is currently
available in essentially identical versions for Mac and PC.

SPV is faster, far more powerful, and easier to use (all menu) than RasMol
or Chime, although it does not have as many different ways to render an
interactive model, and does not support scripted animations. The program is
an excellent first program for undergraduate biochemistry students, being
very easy for beginners, yet powerful enough to carry students into
structural comparison (display, superimpose, and compare many models),
assessment of model quality (both crystal and NMR structures), and advanced
structural analysis, including homology modeling (send jobs to, and
retrieve from, SwissModel). You can also prepare, send, and retrieve jobs
for energy minimization by CHARMM, GROMOS, or AMBER, if available on a
local Unix computer. Finally, you can render stunning graphics for the web
or printing, using QuickDraw3D within SPV, or using POV-Ray, a separate,
free ray-tracing program.

For a more thorough comparison of SPV and RasMol, see

http://macweb.acs.usm.maine.edu/chemistry/GR/GraphicsGallery/Which%3F.html

Learn more about SPV at

http://www.pdb.bnl.gov/expasy/spdbv/mainpage.html.

(SGI users: check the bottom of the "download" page for news about release
of the Unix version.)

I provide a full tutorial for SPV beginners -- and all modeling beginners
-- at

http://macweb.acs.usm.maine.edu/chemistry/GR/SPVTut/text/SPVFrame.html

Thiis tutorial has been thoroughly tested by students.

Cheers!

*****************************

Gale Rhodes   mailto:rhodes@usm.maine.edu
http://macweb.acs.usm.maine.edu/chemistry/GR/GRHomePage.html
Professor of Chemistry
Chemistry Department
University of Southern Maine
PO Box 9300
Portland, Maine 04104-9300
Phone: (207)780-4734 (W)
Fax:   (207)780-5607 (W)

++++------+------+------+------+------+------+------+------+------+------+
From: <slaton@surfnetusa.com>
Subject: Re: Chime 2 slow move bug
Date: Sun, 8 Nov 1998 22:19:23 -0800
To: "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>

I'm not convinced that this is a bug. On Chime 1 there was a great 
disparity between move and delay speeds between PC and Mac platforms. My 
experience is that a given move or delay command is executed 
significantly faster on Chime 1/Mac than Chime 1/PC or Chime2/PC. Perhaps 
this slower move/delay feature being seen in Chime2/Mac brings it into 
parity with the move/delay speeds for Chime on PC. 

Has anyone compared Chime 2 final between Mac and PC's in regards to the 
move and delay speeds? The reports I have seen so far are only between 
Chime 1 and Chime 2 final/beta on Mac. 

regards,
Slaton Lipscomb

C4: Computers in Chemistry at Cabrillo College
http://c4.cabrillo.cc.ca.us/

On 11/8/98 11:59 AM Jens Grabenstein wrote:

>>I am also using a Mac G3 and have experienced the slow "move" and "delay"
>>command responses in Chime 2.0 using scripts that work fine in Chime 2
>>beta, so I suspect it is a problem with Chime 2.0 - But has anyone yet
>>checked this out who is not using a G3?
>>
>>Frieda
>
>I am using a PowerMac 7600 with a 604-processor. And it is terriblely 
>slow. It just worked fine with Chime 1.

        "Rasmol Email List" <rasmol@dhcp-srv2.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Jens Grabenstein <Jens.Grabenstein@konstanz.netsurf.de>
Subject: Re: Chime 2 slow move bug
Date: Mon, 9 Nov 1998 09:45:35 +0100
To: <rasmol@dhcp-srv2.oit.umass.edu>,

>I'm not convinced that this is a bug. On Chime 1 there was a great 
>disparity between move and delay speeds between PC and Mac platforms. My 
>experience is that a given move or delay command is executed 
>significantly faster on Chime 1/Mac than Chime 1/PC or Chime2/PC. Perhaps 
>this slower move/delay feature being seen in Chime2/Mac brings it into 
>parity with the move/delay speeds for Chime on PC. 
>
>Has anyone compared Chime 2 final between Mac and PC's in regards to the 
>move and delay speeds? The reports I have seen so far are only between 
>Chime 1 and Chime 2 final/beta on Mac. 

I compared. I am working with Chime 2 on a Compaq Armada with a 266 
MHz-Processor. The delays are much shorter than on the Mac. The whole 
tutorial I did runs perfect with Chime 2 on the Compaq as it did before 
with Chime 1. But running the same tutorial on the Mac is impossible 
because delays and move commands are very slow. However, it works great 
with Chime 1.

Jens

The optimist believes we live in the best of all worlds;
the pessimist fears this is so.
-----------------------------------------------------------
Visit my website: http://www.konstanz.netsurf.de/~grabenst
-----------------------------------------------------------
E-mail: Jens.Grabenstein@konstanz.netsurf.de
            Jens.Grabenstein@uni-konstanz.de
-----------------------------------------------------------
Made with an Apple Macintosh, the only computer brand

++++------+------+------+------+------+------+------+------+------+------+
From: timp@vt.edu (Timothy L. Pickering)
Subject: Problems with Chime 2.0
Date: Mon, 9 Nov 1998 08:45:15 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Rasmolians,

My week-end project was to download the widely announced new version of
Chime and try it out.  About the only thing I learned was that the old
adage, "never buy/use the *.0 version of any software", remains true.

I have a windows 95 machine with 32 Mb of Ram and a 166 MHz Pentium
processor.  The download and installation were uneventful.  I removed the
old version of Chime as instructed.  Then I set out to explore the
demonstration pages at the MDLI web site.  The "sample Chime page" worked
just fine.  However, when I tried to look at some of the "Demonstration"
pages, virtually every one of them I tried bombed my computer, especially
the multiple models from nmr page, and the solvent accessible surface page.
After three or four tries requiring complete re-boot of my system, I gave
up.

There may be some advantage in moving to version 2.0 of Chime for those
that are dedicated users, but for the occasional user, like me, I don't see
any advantage at this point.  I will be interested in following the
progress and experiences of others as they try to implement the new
version.

Tim Pickering
Virginia Tech

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Problems with Chime 2.0
Date: Sun, 08 Nov 1998 21:41:03 -0500
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: jch@mdli.com, FranklinA@mdli.com

At 11/9/98, you wrote:
>I have a windows 95 machine with 32 Mb of Ram and a 166 MHz Pentium
>processor.  The download and installation were uneventful.  I removed the
>old version of Chime as instructed.  Then I set out to explore the
>demonstration pages at the MDLI web site.  The "sample Chime page" worked
>just fine.  However, when I tried to look at some of the "Demonstration"
>pages, virtually every one of them I tried bombed my computer, especially
>the multiple models from nmr page, and the solvent accessible surface page.
>After three or four tries requiring complete re-boot of my system, I gave
>up.
>
>Tim Pickering
>Virginia Tech

I am using a similar computer: 150 MHz Pentium (I) with 32 Mb RAM and Win95
(not NT, not 98). I just verified that I can run the two demos from MDL's
site above uneventfully. I have been running these and the other demos
routinely, as well as continuing my usual development, with no crash problems.

What version of Navigator were you using? (Help, About communicator)
Did you verify with Chime's menu (About) that you are running version 2.0?

Could you please describe in detail what operation you were doing, and what
message if any or behavior occurs when your computer 'bombs'?

BTW, I never uninstall the old version of Chime simply because I have Nav
3.01, 4.04, 4.06, 4.07 all installed, with Chime 1, Chime 1, Chime 2 beta
4, and Chime 2.0 respectively. But I doubt that this is relevant, except to
say that I haven't seen any reason to follow the instruction from MDL to
uninstall. I just install 'over' the old install (overwriting it). I do
this because with Navigator, I have found that uninstalling one version
while leaving others installed usually leads to problems.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: "Brian White" <brian.white@umb.edu>
Subject: Putting coordinates in scripts?
Date: Mon, 09 Nov 1998 10:49:22 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Hi -
    Is it possible to send chime a script that includes atomic
coordinates (not a file with them, but the coordiantes as text) to add
to the existing view?

Brian

++++------+------+------+------+------+------+------+------+------+------+
From: timp@vt.edu (Timothy L. Pickering)
Subject: Re: Problems with Chime 2.0
Date: Mon, 9 Nov 1998 11:16:26 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

I am running Netscape 3.04.  I verified that Chime 2.0 was running by
looking at the "About plug-ins" window.  When the problems occured, I got
the "Netscape has performed and illegal operation" page fault error
message.  The program is then automatically closed by Windows.

I have copied down the diagnostic information, but don't have it available
on my office machine.  Can provide it later if it would help.

Tim Pickering
===========>

Eric Martz replied to my problem report as follows:
>
>I am using a similar computer: 150 MHz Pentium (I) with 32 Mb RAM and Win95
>(not NT, not 98). I just verified that I can run the two demos from MDL's
>site above uneventfully. I have been running these and the other demos
>routinely, as well as continuing my usual development, with no crash problems.
>
>What version of Navigator were you using? (Help, About communicator)
>Did you verify with Chime's menu (About) that you are running version 2.0?
>
>Could you please describe in detail what operation you were doing, and what
>message if any or behavior occurs when your computer 'bombs'?
>
>BTW, I never uninstall the old version of Chime simply because I have Nav
>3.01, 4.04, 4.06, 4.07 all installed, with Chime 1, Chime 1, Chime 2 beta
>4, and Chime 2.0 respectively. But I doubt that this is relevant, except to
>say that I haven't seen any reason to follow the instruction from MDL to
>uninstall. I just install 'over' the old install (overwriting it). I do
>this because with Navigator, I have found that uninstalling one version
>while leaving others installed usually leads to problems.
>
>-Eric

References: <36470F00.B4F3B353@umb.edu>
X-Accept-Language: en
++++------+------+------+------+------+------+------+------+------+------+
From: Arne Mueller <a.mueller@icrf.icnet.uk>
Subject: Re: Putting coordinates in scripts?
Date: Mon, 09 Nov 1998 16:21:05 +0000
To: brian.white@umb.edu
Cc: rasmol@dhcp-srv2.oit.umass.edu

Brian White wrote:
> 
> Hi -
>     Is it possible to send chime a script that includes atomic
> coordinates (not a file with them, but the coordiantes as text) to add
> to the existing view?
> 
> Brian

Hi,

I know how to do this in rasmol (but this may not work as an addition to
your existing view):

the formalism is as follows:

load pdb inline
rasmol_commands
exit
contents_of_pdb_file

here's an example:

load pdb inline
select phe,trp,his,tyr
spacefill
exit
ATOM      1  N   THR     1      17.047  14.099   3.625  1.00 13.79
ATOM      2  CA  THR     1      16.967  12.784   4.338  1.00 10.80
ATOM      3  C   THR     1      15.685  12.755   5.133  1.00  9.19
[...]

have a look at http://ftp.gwdg.de/pub/misc/rasmol/v2.6beta/release.txt
section "[4.4]  Storing Atom Co-ordinates in Scripts"

	greetings,

	Arne

-- 
Arne Mueller
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX, U.K.
phone : +44-(0)171 2693405      | Fax : +44-(0)171 269 3258
email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/

X-Authentication-Warning: fir.lif.icnet.uk: turcotte set sender to M.Turcotte@icrf.icnet.uk using -f
++++------+------+------+------+------+------+------+------+------+------+
From: Marcel Turcotte <M.Turcotte@icrf.icnet.uk>
Subject: Problem with .rasmolrc?
Date: Mon, 9 Nov 1998 16:23:24 GMT
To: rasmol@dhcp-srv2.oit.umass.edu

Hello all,

Say I have the following .rasmolrc file:

----------------------------------------------------------------------
echo "loading .rasmolrc ..."

define int (phe,ala,met,ile,leu,tyr,val,trp)
define surf (lys,arg,glu,asn,asp)
define fun (cys,his,gln,set,thr)
define parse (pro,gly)

echo "done"
----------------------------------------------------------------------

In the following 3 scenarios the .rasmolrc file is loaded (I can see
the loading .rasmolrc line on the screen), but only in the first one
do I get access to the defined sets.  Is this the expected behavior?
Or is this a known problem?  Any work around?  Of course I can source
the script afterwords but it becomes tedious after the 200th molecule
...

Any help would be appreciated,
Marcel

----------------------------------------------------------------------
Scenario 1:

$ rasmol pdb121p.ent

RasMol Molecular Renderer
Roger Sayle, August 1995
Version 2.6
[8bit version]

Molecule name ....... H-RAS P21 PROTEIN COMPLEX WITH GUANOSINE-5'-[B,G-METHYLENE]
Classification ...... ONCOGENE PROTEIN
Secondary Structure . PDB Data Records
Brookhaven Code ..... 121P
Number of Chains .... 2
Number of Groups .... 166 (197)
Number of Atoms ..... 1322 (228)
Number of Bonds ..... 38
Number of Helices ... 5
Number of Strands ... 6
Number of Turns ..... 6
Number of Bonds ..... 1375

RasMol> 
loading .rasmolrc ...
done
RasMol> select parse
select parse
65 atoms selected!
----------------------------------------------------------------------
Scenario 2:

$ rasmol -script script.rasmol 

RasMol Molecular Renderer
Roger Sayle, August 1995
Version 2.6
[8bit version]

RasMol> 
loading .rasmolrc ...
done
RasMol> select parse
select parse
No atoms selected!

where script.rasmol is 

load pdb pdb121p.ent
----------------------------------------------------------------------
Scenario 3:

$ rasmol

RasMol Molecular Renderer
Roger Sayle, August 1995
Version 2.6
[8bit version]

RasMol> 
loading .rasmolrc ...
done
RasMol> load pdb121p.ent
load pdb121p.ent
Molecule name ....... H-RAS P21 PROTEIN COMPLEX WITH GUANOSINE-5'-[B,G-METHYLENE]
Classification ...... ONCOGENE PROTEIN
Secondary Structure . PDB Data Records
Brookhaven Code ..... 121P
Number of Chains .... 2
Number of Groups .... 166 (197)
Number of Atoms ..... 1322 (228)
Number of Bonds ..... 38
Number of Helices ... 5
Number of Strands ... 6
Number of Turns ..... 6
Number of Bonds ..... 1375

RasMol> select parse
select parse
No atoms selected!
----------------------------------------------------------------------

-- 
Marcel Turcotte                          Biomolecular Modelling Laboratory
M.Turcotte@icrf.icnet.uk                 Imperial Cancer Research Fund
[44|0]-171-269-3348/3258 Phone/Fax       PO Box 123, 44 Lincoln's Inn Fields
http://www.icnet.uk/bmm/people/turcotte  London WC2A 3PX, England

++++------+------+------+------+------+------+------+------+------+------+
From: Dan Roseman <drose07@sneezey.bimcore.emory.edu>
Subject: toggling rasmol scripts
Date: Mon, 9 Nov 1998 12:31:58 -0500 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu

Hello,

Is there a way to use a single button (TYPE=submit) that would
cycle through multiple Rasmol/Chime scripts?  I've been able to toggle
between two scripts using one button based upon javascripts written by Dr.
Martz.  This most likely requires some javascripting as well.  Thanks.

++++------+------+------+------+------+------+------+------+------+------+
From: Srinivas C Turaga <sturaga@student.umass.edu>
Subject: Re: Problems with Chime 2.0
Date: Mon, 09 Nov 1998 13:06:48 -0500 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: franklina@mdli.com

Dear Tim,
	Although Netscape version 3.04 is *supposed* to work, according
to the Chime release notes, I would strongly recommend that you upgrade to
the latest browser (Netscape 4.5). I can verify that Chime 2.0 works just
fine with this combination.
	It is the browser IMO that is causing all your problems.

/Srinivas Turaga

On Mon, 9 Nov 1998, Timothy L. Pickering wrote:

> I am running Netscape 3.04.  I verified that Chime 2.0 was running by
> looking at the "About plug-ins" window.  When the problems occured, I got
> the "Netscape has performed and illegal operation" page fault error
> message.  The program is then automatically closed by Windows.
> 
> I have copied down the diagnostic information, but don't have it available
> on my office machine.  Can provide it later if it would help.
> 
> Tim Pickering
> ===========>
> 
> Eric Martz replied to my problem report as follows:
> >
> >I am using a similar computer: 150 MHz Pentium (I) with 32 Mb RAM and Win95
> >(not NT, not 98). I just verified that I can run the two demos from MDL's
> >site above uneventfully. I have been running these and the other demos
> >routinely, as well as continuing my usual development, with no crash problems.
> >
> >What version of Navigator were you using? (Help, About communicator)
> >Did you verify with Chime's menu (About) that you are running version 2.0?
> >
> >Could you please describe in detail what operation you were doing, and what
> >message if any or behavior occurs when your computer 'bombs'?
> >
> >BTW, I never uninstall the old version of Chime simply because I have Nav
> >3.01, 4.04, 4.06, 4.07 all installed, with Chime 1, Chime 1, Chime 2 beta
> >4, and Chime 2.0 respectively. But I doubt that this is relevant, except to
> >say that I haven't seen any reason to follow the instruction from MDL to
> >uninstall. I just install 'over' the old install (overwriting it). I do
> >this because with Navigator, I have found that uninstalling one version
> >while leaving others installed usually leads to problems.
> >
> >-Eric
> 
> 

References: <v01510103b26cb67cde3c@[128.173.164.24]>
++++------+------+------+------+------+------+------+------+------+------+
From: "Andy Tucker" <tuckera@Rex.queens.edu>
Subject: Chime 2.0 and Netscape 3.04
Date: Mon, 9 Nov 1998 15:24:49 EST
To: rasmol@dhcp-srv2.oit.umass.edu

I am successfully running Chime 2.0 w/Netscape 2.04.
I did get an error when I first installed it and tried to run the 
demos.  However, I then rebooted the machine and have run 4 of the 
demos without problems.

I did not have any version of Chime installed before, if that makes a 
difference.
andy

Dr. W. Andrew Tucker            Queens College Chem. Dept.
tuckera@rex.queens.edu          1900 Selwyn Ave.
(704)337-2317                   Charlotte, NC 28277

++++------+------+------+------+------+------+------+------+------+------+
From: Frieda Reichsman <friedar@biochem.umass.edu>
Subject: Sprouting only some hydrogens
Date: Mon, 9 Nov 1998 18:20:03 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Does anyone know if it's possible to limit the display of sprouted
hydrogens (in Chime 2) to only one part of a protein? I have tried many
variations/orders of things like:

"sprout hydrogen
restrict backbone
spacefill 180"

and

"select backbone
sprout hydrogen"

etc., etc., all of which yield either no hydrogens displayed, or all the
hydrogens in the entire molecule displayed. I am using MacG3/Netscape4.5...

Thanks,

Frieda

_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Frieda Reichsman, Ph.D.                       _/_/_/_/_/
Biochemistry and Molecular Biology            _/_/_/_/_/
University of Massachusetts                   _/_/_/_/_/
Amherst, MA 01003                             _/_/_/_/_/
email: friedar@biochem.umass.edu              _/_/_/_/_/
Phone: (413) 545-4029                         _/_/_/_/_/
Fax:   (413) 545-3291                         _/_/_/_/_/
Voice mail: (413) 545-4025                    _/_/_/_/_/
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

References: <199811072004.UAA28196@giasmda.vsnl.net.in>
++++------+------+------+------+------+------+------+------+------+------+
From: Marc Saric <Marc.Saric@rz.ruhr-uni-bochum.de>
Subject: Re: Chime 2 is available
Date: Sun, 08 Nov 1998 10:23:03 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

K. Arun wrote:

> Hi,
>         I do apologise if this is an FAQ, but is Chime (any version)
> available on the Linux/UNIX platform for Netscape
> Navigator/Communicator. If not, are there any plans for a port ?

According to their download-pages, there are apparently no plans for
UNIX-ports of any kind (even not SGI wich should be a quite wide-spread
platform in the molecular-graphics-area).

Unfortunately!

-- 

Bye,

Marc Saric

Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/

Visit the FS98 3D-accelerators FAQ at
http://www.simflight.com/marc

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++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Fwd: Timing bug in Mac Chime 2
Date: Tue, 10 Nov 1998 10:47:45 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

>From: Franklin Adler <Franklina@mdli.com>
>To: "'Eric Martz'" <emartz@microbio.umass.edu>
>Subject: FW: Chime 2 is available
>Date: Tue, 10 Nov 1998 12:47:56 -0800
>
>Eric,
>
>We are able to reproduce the move and delay performance problems reported by
>several rasmol list members in Chime for the Mac. We are currently looking
>into this. At this time there aren't any work arounds for increasing the
>performance using these commands. You may want to inform your rasmol list
>members that we are aware of this problem.
>
>-Franklin
>

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

Content-Disposition: inline
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++++------+------+------+------+------+------+------+------+------+------+
From: Jean Debord <JDebord@compuserve.com>
Subject: Lipophilicity potential in Chime
Date: Wed, 11 Nov 1998 01:17:02 -0500
To: Rasmol List <rasmol@dhcp-srv2.oit.umass.edu>

Dear Colleagues,

I am using Chime 2.0 to display the molecular lipophilicity potential of
small molecules. I have some questions :

1) Which set of atomic lipophilicities is used? (e.g. Broto/Moreau,
Crippen...). Is there a bibliographic reference available?

2) What is the difference between "Relative MLP coloring" and "Absolute MLP
coloring"? 

3) How can I get the Log P of the molecule?

4) Is it possible to obtain the Log P of a selected set of atoms?

5) Is it possible to display the MLP without drawing a molecular surface
first?

Thanks in advance.

Jean Debord
Laboratoire de Pharmacologie, Faculte de Medecine
2 Rue du Docteur Marcland, 87025 Limoges, France
http://ourworld.compuserve.com/homepages/JDebord

References: <Version.32.19981110103633.00deb460@marlin.bio.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: William R Mcclure <wm0p+@andrew.cmu.edu>
Subject: Re: Timing bug in Mac Chime 2
Date: Wed, 11 Nov 1998 08:22:44 -0500 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu

Excerpts from mail: 10-Nov-98 Fwd: Timing bug in Mac Chime 2 by Eric
Martz@microbio.umas 
> >We are able to reproduce the move and delay performance problems reported by
> >several rasmol list members in Chime for the Mac. We are currently looking
> >into this. At this time there aren't any work arounds for increasing the
> >performance using these commands. You may want to inform your rasmol list
> >members that we are aware of this problem.

  I hope MDL can fix this problem soon because any page with a 'move'
command is essentially unviewable with Chime 2.0.  Moreover, most of the
additional testing/experience with the v2.0 features on the Mac that I'd
like to do can't be done until those pages are viewable.
  That, however, is not the only problem with timing using Mac versions
of Chime.  The comment below was sent to MDL after trying out
v2.0(Mac-beta1). I include it here because I wonder whether other Mac
users of v1.0 (or Windows users for that matter) have actually timed the
'spiny' and 'delay' commands.  I realize the "observed speed" can be
slower than specified, but I find it to be faster in many circumstances
with several hardware/software combinations (PowerMac 7500 & G3; MacOS:
7.1, 7.5 & 8.1; Nav 3.01 & 4.05; and Chime 1.0 & 2.0)

 -Will McClure

*****
Comment sent to MDL (9/24/98):
>From your Embed Tag Reference:  Spin y "Specifies the rotation speed
along the Y-axis (vertical axis) in degrees per second. The default is
30."
At your site, the pharm.html page has 'spiny=40' in the EMBED statement.
This should result in1 revolution in 9 seconds or about 7 per min. I
found that it rotated 20 times in one minute.
I understand the point that the speed can be slower than specified
because of computer speed, but why does it go faster than specified?
This has been my experience with Chime 1.0 also. 

X-MSMail-Priority: Normal
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++++------+------+------+------+------+------+------+------+------+------+
From: Henry Brzeski <h.brzeski@herts.ac.uk>
Subject: Radio buttons that work
Date: Thu, 12 Nov 1998 08:34:50 -0000
To: rasmol <rasmol@dhcp-srv2.oit.umass.edu>

To all 2 chimers

I have been experimenting with our wonderful new present (Chime2) and had
trouble implementing the radio button capability. I had a play with the code
and found the following to work.

The following displays 3 buttons one of which stays depressed when pushed
but can be 'un-depressed' by pushing another button. If a button which is
being depressed has an altscript tag attached this will be executed when the
next button is depressed eg using the example below if the cartoon button is
depressed after wireframe the cartoon is coloured grey but if it is
depressed after spacefill it is coloured green. Hope this is of some use to
you all.

<p align="center">Spacefill <embed type="application/x-spt" width="15"
height="15"
script="select not water; wireframe off; cartoon off; spacefill on; colour
cpk" altscript="select all; colour green" button="radio" name="radio1"
target="themol"></p>

<p align="center">Wireframe <embed type="application/x-spt" width="15"
height="15"
script="select not water; wireframe on; cartoon off; spacefill off; colour
cpk"
button="radio" name="radio2" target="themol"></p>

<p align="center">Cartoon <embed type="application/x-spt" width="15"
height="15"
script="select not water; wireframe off; cartoon on; spacefill off; colour
cpk"
button="radio" name="radio3" target="themol"></p>

Henry Brzeski
Department of Biosciences
College Lane
Hatfield
HERTFORDSHIRE
AL10 9AB

Phone : 01707 284554
Fax   : 01707 285046

X-MSMail-Priority: Normal
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4
++++------+------+------+------+------+------+------+------+------+------+
From: Henry Brzeski <h.brzeski@herts.ac.uk>
Subject: Working with and displaying ISIS/Draw files
Date: Thu, 12 Nov 1998 08:34:51 -0000
To: rasmol <rasmol@dhcp-srv2.oit.umass.edu>

To all 2 chimers

I was trying to load 2D drawings (skc files) and view them in 3D.
Unfortunately all I get are molecules that have been run over by a steam
roller. This is true even when I use a file drawn by the MDL team that has
non planar bonds eg Adribosp.skc.

Another file that comes with ISIS/Draw is Boat.skc. Drawn in 2D this might
be a fair representation of a boat type structure but by the time it goes
through select all;spacefill on and is then rendered in 3D (via the short
menu) it is not very convincing.

Is there any way I can get true 3D from these drawings?

Henry Brzeski
Department of Biosciences
College Lane
Hatfield
HERTFORDSHIRE
AL10 9AB

Phone : 01707 284554
Fax   : 01707 285046

++++------+------+------+------+------+------+------+------+------+------+
From: "Tamas Gunda" <tamasgunda@tigris.klte.hu>
Subject: 2D/3D sketches
Date: Thu, 12 Nov 1998 14:37:26 +1
To: rasmol@dhcp-srv2.oit.umass.edu

>I was trying to load 2D drawings (skc files) and view them in 3D.
>Unfortunately all I get are molecules that have been run over by a steam
>roller. This is true even when I use a file drawn by the MDL team that has
>non planar bonds eg Adribosp.skc.

Chime does not have built 2D-->3D converter, therefore 3D images appear
only if the input molfile contains a 3D structure. But most of the
modeling programs can save files in 3D MDL mol format, and these can be
implanted into sketches. 

Tamas Gunda

 

************************************************************************
   Dr Tamas E. Gunda                   phone: (+36-52) 316666-2479
   Research Group of Antibiotics       fax  : (+36-52) 310936
   L. Kossuth University               e-mail: tamasgunda@tigris.klte.hu
   POBox 36                            http://www.klte.hu/~gundat               
   H-4010 Debrecen
   Hungary
************************************************************************

++++------+------+------+------+------+------+------+------+------+------+
From: Javier Zuniga <jzuniga@pehuenche.secom.utalca.cl>
Subject: Re: Radio buttons that work
Date: Thu, 12 Nov 1998 11:19:52 -0300
To: rasmol@dhcp-srv2.oit.umass.edu

At 08:34 12/11/98 -0000, you wrote:
>To all 2 chimers
>
>I have been experimenting with our wonderful new present (Chime2) and had
>trouble implementing the radio button capability. I had a play with the code
>and found the following to work.
>
>The following displays 3 buttons one of which stays depressed when pushed
>but can be 'un-depressed' by pushing another button. If a button which is
>being depressed has an altscript tag attached this will be executed when the
>next button is depressed eg using the example below if the cartoon button is
>depressed after wireframe the cartoon is coloured grey but if it is
>depressed after spacefill it is coloured green. Hope this is of some use to
>you all.
>
><p align="center">Spacefill <embed type="application/x-spt" width="15"
>height="15"
>script="select not water; wireframe off; cartoon off; spacefill on; colour
>cpk" altscript="select all; colour green" button="radio" name="radio1"
>target="themol"></p>
>
><p align="center">Wireframe <embed type="application/x-spt" width="15"
>height="15"
>script="select not water; wireframe on; cartoon off; spacefill off; colour
>cpk"
>button="radio" name="radio2" target="themol"></p>
>
><p align="center">Cartoon <embed type="application/x-spt" width="15"
>height="15"
>script="select not water; wireframe off; cartoon on; spacefill off; colour
>cpk"
>button="radio" name="radio3" target="themol"></p>
>
>
>Henry Brzeski
>Department of Biosciences
>College Lane
>Hatfield
>HERTFORDSHIRE
>AL10 9AB
>
>Phone : 01707 284554
>Fax   : 01707 285046
>

Dear Henry:

I'm new to the mail-list, so I don't know if this reply is going to every
one or just to you. My question is quite simple: What Nav/Communicator
version where you using with Chime 2 when you tested your radio buttons?.
Also, was it ran over a PC? How many RAM, CPU speed? I'd like to suggest
that everyone reporting a new Chime trick should inform the
Nav/Communicator-Chime combination used and the basic system
characteristics, since we all know there are combination and/or platform
problems with Chime 2. 

Bye.

                                Javier.

(any free, good english course on the web? :)

--------------------------------------------------------------------
Javier Zuniga Rebolledo
Instituto de Biologia Vegetal y Biotecnologia
IBVB - Universidad de Talca CHILE
Fono: (56)-71-200280
Fax:  (56)-71-200276
e-mail: jzuniga@pehuenche.utalca.cl
--------------------------------------------------------------------

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++++------+------+------+------+------+------+------+------+------+------+
From: "PENUELAS SANCHEZ, Ivan" <ipenuelas@unav.es>
Subject: Can you send me ch20w32.exe?
Date: Fri, 13 Nov 1998 10:28:49 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

I´ve been reading all your comments about the great improvements of the
new version of Chime. I've been trying to download the self-extracting
installation file for more than a week but I'm always hung! Could
anybody e-mail me the file ch20w32.exe (that's the  Windows 95/NT
version)??
Thanks.

Iván Peñuelas
Macromolecular structure assistant professor
University of Navarra
Pamplona
Spain

X-MSMail-Priority: Normal
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++++------+------+------+------+------+------+------+------+------+------+
From: Henry Brzeski <h.brzeski@herts.ac.uk>
Subject: RE: Radio buttons that work
Date: Fri, 13 Nov 1998 11:56:14 -0000
To: rasmol <rasmol@dhcp-srv2.oit.umass.edu>

Javier

> I'm new to the mail-list, so I don't know if this reply is going to every
> one or just to you. My question is quite simple: What Nav/Communicator
> version where you using with Chime 2 when you tested your radio buttons?.

This is a JavaScript problem as the PC works when you  get the JavaScript
right.

> Also, was it ran over a PC? How many RAM, CPU speed? I'd like to suggest
> that everyone reporting a new Chime trick should inform the
> Nav/Communicator-Chime combination used and the basic system
> characteristics, since we all know there are combination and/or platform

Since you asked it was a PC with a 233 AMD chip, 64Mb RAM, 4.05 Netscape
Chime 2

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++++------+------+------+------+------+------+------+------+------+------+
From: "PENUELAS SANCHEZ, Ivan" <ipenuelas@unav.es>
Subject: Chime 2 already received
Date: Tue, 17 Nov 1998 11:40:43 +0100
To: rasmol@dhcp-srv2.oit.umass.edu

I've already received Chime 2 from Eric Martz. 
Please do not send me more copies of the file. 
Thanks for your collaboration.

Iván Peñuelas
Macromolecular structure assistant professor
University of Navarra
Pamplona
Spain

++++------+------+------+------+------+------+------+------+------+------+
From: Alexander Garcia <acad@accefyn.org.co>
Subject: Screen Refresh
Date: Tue, 17 Nov 1998 10:27:31 -0500
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

Hi there! I have worked with Raswin and I have used BorlandC but I have
had some problenms with the refresh of the screen. At the top, it is
like a TV with interference and I do not know what happen. Someone knows

if it is a problem of BorlandC? Someone knows the solution? Please, I
need your help. Thanks in advance, cheers.

        Rasmol List <rasmol@dhcp-srv2.oit.umass.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Tim Maffett <tim@mdli.com>
Subject: Re: Lipophilicity potential in Chime
Date: Wed, 18 Nov 1998 02:00:38 -0800
To: rasmol@dhcp-srv2.oit.umass.edu,

  I will follow this reply with a more 'detailed' list of information.

At 01:17 AM 11/11/98 -0500, Jean Debord wrote:
>Dear Colleagues,
>
>I am using Chime 2.0 to display the molecular lipophilicity potential of
>small molecules. I have some questions :
>
>1) Which set of atomic lipophilicities is used? (e.g. Broto/Moreau,
>Crippen...). Is there a bibliographic reference available?
>
>2) What is the difference between "Relative MLP coloring" and "Absolute MLP
>coloring"? 

  see the references in message that follows this reply.  
The relative/absolute coloring is from the Gaillard paper (I think ;).

>
>3) How can I get the Log P of the molecule?

 "show mlp"
command will do this, but you must first color dots or surface with MLP.
("color dots MLP" to color dots)

>
>4) Is it possible to obtain the Log P of a selected set of atoms?

  The Charge calculations are done for only the selected atoms, but
my LogP stuff looks at the entire molecule (this could be fixed
at some point...)

>
>5) Is it possible to display the MLP without drawing a molecular surface
>first?

 again, you can "color dots mlp" instead.

>
>Thanks in advance.
>
>Jean Debord
>Laboratoire de Pharmacologie, Faculte de Medecine
>2 Rue du Docteur Marcland, 87025 Limoges, France
>http://ourworld.compuserve.com/homepages/JDebord
>
>

        Rasmol List <rasmol@dhcp-srv2.oit.umass.edu>
  also]
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++++------+------+------+------+------+------+------+------+------+------+
From: Tim Maffett <tim@mdli.com>
Subject: Re: Lipophilicity potential in Chime [MORE detailed info, MEP
Date: Wed, 18 Nov 1998 02:00:48 -0800
To: rasmol@dhcp-srv2.oit.umass.edu,

This is some misc. info I have thrown together (literally!) -
hope it helps... it contains the references.

-----

 There are several distance functions you can use for MLP and MEP
mapping.  The chime script commands are:

   "set mlp function [1|Gaillard|2|Audry|3|Fauchere|4|Hartshorn]
(default=Gaillard (1))"
   "set mep function [1|Gaillard|2|Audry|3|Fauchere|4|Hartshorn|5|Coulomb]
(default=Coulomb (5))"

  The references to these distance functions can be found below (with
the exception of the Hartshorn function, which Michael Hartshorn from
our Chime group developed).
   The default coloring for Molecular Lipophilicity Potential (MLP)
surfaces is from Journal of Computer-aided Molecular Design, 9 (1994) 83-96
(Patrick Gaillard, Pierre-Alain Carrupt, Bernard Testa, and Alain Boudon)

  The LogP calculations in chime are based on my implementation of 
an algorithm described in:

"A New Atom-Additive Method for Calculating Partition Coefficients"
Wang, R.X.; Fu, Y.; Lai, L.H.  J.Chem.Inf.Comput.Sci., 1997, 37, 615-621.

  

---

(Most of the info below is taken from my comments within the Code,
I think it is fairly clear though..)

More Commands dealing with MLP/MEP
/*
   set the absolute/relative computation of
   texture map values

   set mlp mode true  : 'absolute' scale (for comparing different mols)
   set mlp mode false:   molecule relative, highest/lowest relevant to
                  current molecule only
                  (this is DEFAULT)
*/
/*
   sets the max distance to be considered for MLP 
      influence calculations.
      default is 4 angstroms

   "set mlp within [distance] #angstroms#"
   or 
   "set mlp distance [within] #angstroms#"

*/
/*
   setting MEP distance function

"set mep function [1|Gaillard|2|Audry|3|Fauchere|4|Hartshorn|5|Coulomb]
(default=Coulomb (5))"
      1 - Gaillard
      2 - Audry
       3 - Fauchere
      4 - Hartshorn weighted
      5 - Coulomb's Law
*/
/*
   set the range for MEP texture mapping

   set mep mode 1               | colored relative to extremes of molecule
   set mep mode 2               | -0.10 to +0.10 range for charges
   set mep mode 3|rasmol      | -0.24 to +0.24 range for charges (what
rasmol uses)
*/
/*
   sets the max distance to be considered for MEP 
      influence calculations.
      default is 8 angstroms

   "set mep|potential distance [within] #angstroms#"
or
   "set mep|potential within [distance] #angstroms#"

*/

You can use these new 'Color Dots' commands (in addition to the 
original rasmol commands):
   "color dots [MLP|MEP]"

('MLP' and 'Potential' are the same thing)

--------

You can SHOW LogP calculations via (info output to message callback): 

"show mlp"

      added "show mlp" command to show the total sum LogP
      for the compound, and the sum (from points on grid/
      VDW surface) of the +/- LogP contributors

  You *MUST* first execute a 'color dots MLP' or color a Molecular
surface with MLP BEFORE this command, as it is the points (dots 
or points on molecular surface) that are used in conjunction with 
the distance functions (see various options provided by above commands)
to calculate the logp.

  The info is reported in the form:

XlogP= ###
Sum MLP + =  ###
Sum MLP - =  ###

  
--------
Commands dealing with new charge calculations

   'set kollman sprout true|false' 
            command to determine if hydrogens will be sprouted 
            for kollman charge calculations, if needed

   /*
      set charge function [none|Gasteiger|Kollman|Charmm]
         or
      set charge <value>
   */

   /*
      we default to NO preferred charge calc method..
         this means that <256 het atoms we use Gasteiger, 
         else we use Kollman partial charges if there are hydrogens
         present (OR we have been told to SPROUT hydrogens), 
         else we assign Charmm19 charges to aminoacids
   */
   Charges are only calculated if there was no b-Values (from PDB file)
LESS THAN 0.

   /*
      IF NOT Kollman Partial Charges (Must be >255 atoms for Kollman,
         and Hydrogens must be present OR sprouted)
      then try and assign Charmm charges, and if that
      doesn't work (no aminoacids present..) then
      do gasteiger
   */

----------------------------------------------------------------------------
Appendix 1: References for Distance functions used in Chime for MLP (or MEP)
mapping.

/*
Audry (et al.) distance function

   MLP = Sum( f / (1 + d) )1-natoms

   f = Lipophilic value for atom i
   d = distance from point to atom (angstroms)

   Audry, E.; Dubost, J. P.; Colleter, J. C.; Dallet, P. 
   A new approach to structure-activity relations: the "molecular
lipophilicity potential". 
   Eur. J. Med. Chem. 1986, 21, 71-72.

   For our purposes function =  f / (250 + d)
   because 1 angstrom is 250 units in our distance system

*/

/*
Gaillard (et al.) distance function

   MLP = Sum( f * e^(-d/2) )1-natoms

   f = Lipophilic value for atom i
   d = distance from point to atom (angstroms)

   Gaillard, P., Carrupt, P.A., Testa, B. and Boudon, A., 
   J.Comput.Aided Mol.Des. 8, 83-96 (1994)

   (Note: distance d is converted FROM rasmol units to Angstroms 
         before exp() call)

*/

/*
Fauchere (et al.) distance function

   MLP = Sum( f * e^(-d) )1-natoms

   f = Lipophilic value for atom i
   d = distance from point to atom (angstroms)

   FauchŠre, J. L.; Quarendon, P.; Kaetterer, L. 
   Estimating and representing hydrophobicity potential. 
   J. Mol. Graphics 1988, 6, 203-206.

   (Note: distance d is converted FROM rasmol units to Angstroms 
         before exp() call)
*/

/*
   Molecular Lipophilicity Potential (MLP) 

   GENERATESURFACE_COLOR_CODE_MLP_GAILLARD

   This color set is from Journal of Computer-aided Molecular Design, 9
(1994) 83-96
      (Patrick Gaillard, Pierre-Alain Carrupt, Bernard Testa, and Alain
Boudon)
*/

++++------+------+------+------+------+------+------+------+------+------+
From: Tim Maffett <tim@mdli.com>
Subject: Re: 2D/3D sketches
Date: Wed, 18 Nov 1998 02:00:59 -0800
To: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu

At 02:37 PM 11/12/98 +1, Tamas Gunda wrote:
>>I was trying to load 2D drawings (skc files) and view them in 3D.
>>Unfortunately all I get are molecules that have been run over by a steam
>>roller. This is true even when I use a file drawn by the MDL team that has
>>non planar bonds eg Adribosp.skc.
>
>Chime does not have built 2D-->3D converter, therefore 3D images appear
>only if the input molfile contains a 3D structure. But most of the
>modeling programs can save files in 3D MDL mol format, and these can be
>implanted into sketches. 

  Chime 2 for the Windows platform does include Sculpt (tm) from Interactive
Simulations, and using sculpt you can play with the molecule and it
will minimize it to some reasonable 3D structure.  Sculpt also lets you
grab atoms and bend the molecule, showing favorable and unfavorable 
interactions.  You can enter the Sculpt mode my using the 'Sculpt Mode'
menu item.  Once you are in sculpt mode click on and atom (and hold the 
mouse) and you can just start moving the mouse around to bend the molecule.
   If you just 'jiggle' the mouse then the molecule will continue
to minimize into some reasonable conformation.
   Also, once you are in the Sculpting mode you get another menu
on the Chime menu which allows you to toggle various options.  You can
also send commands using Chime scripting language...

  For more info on Sculpt you can visit their web site at
http://www.intsim.com/chime.html  (this can also be reached from
clicking in the Chime about box).

-tim

>
>Tamas Gunda
>
> 
>
>************************************************************************
>   Dr Tamas E. Gunda                   phone: (+36-52) 316666-2479
>   Research Group of Antibiotics       fax  : (+36-52) 310936
>   L. Kossuth University               e-mail: tamasgunda@tigris.klte.hu
>   POBox 36                            http://www.klte.hu/~gundat
     
>   H-4010 Debrecen
>   Hungary
>************************************************************************
>
>

X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by dhcp-srv2.oit.umass.edu id JAA28848
++++------+------+------+------+------+------+------+------+------+------+
From: Jean Richelle <jean@ucmb.ulb.ac.be>
Subject: Please tell me
Date: Wed, 18 Nov 1998 15:41:13 +0100 (MET)
To: rasmol@dhcp-srv2.oit.umass.edu

Is this list a place where postdoctoral position (in MD and protein-ligand
interaction study) can be announced ?

_____________________________________________________________________________
Jean Richelle <jean@ucmb.ulb.ac.be>
Unité de Conformation des Macromolécules Biologiques   Tel: +32 (0)2 650 3587
Université libre de Bruxelles                          FAX: +32 (0)2 648 8954
av. FD Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium
_____________________________________________________________________________

X-pmrqc: 1
++++------+------+------+------+------+------+------+------+------+------+
From: "Michael Meredith" <michael.meredith@continuing-education.oxford.ac.uk>
Subject: Re: Please tell me
Date: Wed, 18 Nov 1998 14:59:01 -0000
To: rasmol@dhcp-srv2.oit.umass.edu

I don't know, but you can try!

Michael

References: <365195E3.1DDD7DE4@accefyn.org.co>
++++------+------+------+------+------+------+------+------+------+------+
From: Alexander Garcia <acad@accefyn.org.co>
Subject: Screen Refresh/please
Date: Wed, 18 Nov 1998 10:25:15 -0500
To: "rasmol@lists.umass.edu" <rasmol@dhcp-srv2.oit.umass.edu>

Please can some one give me a hand with it....please

Alexander Garcia wrote:

> Hi there! I have worked with Raswin and I have used BorlandC but I
> have
> had some problenms with the refresh of the screen. At the top, it is
> like a TV with interference and I do not know what happen. Someone
> knows
>
> if it is a problem of BorlandC? Someone knows the solution? Please, I
> need your help. Thanks in advance, cheers.

 e>
X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id NAA05172
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Please tell me
Date: Thu, 19 Nov 1998 01:51:12 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Yes. Either send the announcement to me to forward, or you can subscribe at

http://www.umass.edu/microbio/rasmol/raslist.htm

At 11/18/98, you wrote:
>Is this list a place where postdoctoral position (in MD and protein-ligand
>interaction study) can be announced ?
>
>_____________________________________________________________________________
>Jean Richelle <jean@ucmb.ulb.ac.be>
>Unité de Conformation des Macromolécules Biologiques   Tel: +32 (0)2 650 3587
>Université libre de Bruxelles                          FAX: +32 (0)2 648 8954
>av. FD Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium
>_____________________________________________________________________________
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Jean Richelle <jean@ucmb.ulb.ac.be>
Subject: 3 Postdoctoral positions
Date: Fri, 20 Nov 1998 09:13:13 +0100 (MET)
To: rasmol@dhcp-srv2.oit.umass.edu
Cc: Shoshana Wodak <shosh@ebi.ac.uk>, Shoshana Wodak <shosh@ucmb.ulb.ac.be>

  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.
  Send mail to mime@docserver.cac.washington.edu for more info.

--1461750973-1478110281-911549593=:16002

Dear all,

Three postdoctoral positions are open in our lab, UCMB - Brussels, Belgium:

   o to develop a knowledge-base on protein-ligand interactions
=09   cf <http://www.ucmb.ulb.ac.be/job1.html> or first attached file

   o to investigage molecular recognition processes in acetylcholinesterase
=09   cf <http://www.ucmb.ulb.ac.be/job2.html> or second attached file

   o in molecular design of peptide vaccines
=09   cf <http://www.ucmb.ulb.ac.be/job3.html> or third attached file

Thank you for your attention,

Jean

___________________________________________________________________________=
__
Jean Richelle <jean@ucmb.ulb.ac.be>
Unit=E9 de Conformation des Macromol=E9cules Biologiques   Tel: +32 (0)2 65=
0 3587
Universit=E9 libre de Bruxelles                          FAX: +32 (0)2 648 =
8954
av. FD Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium
___________________________________________________________________________=
__

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--1461750973-1478110281-911549593=:16002--

++++------+------+------+------+------+------+------+------+------+------+
From: Dan Roseman <drose07@sneezey.bimcore.emory.edu>
Subject: Re: toggling rasmol scripts
Date: Fri, 20 Nov 1998 11:24:04 -0500 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu

> 
> Is there a way to use a single button (TYPE=submit) that would
> cycle through multiple Rasmol/Chime scripts?  I've been able to toggle
> between two scripts using one button based upon javascripts written by Dr.
> Martz.  This most likely requires some javascripting as well.  Thanks.

Thanks to some responses, I have some answers that one might be interested
in knowing.  The problem of cycling through a series of Rasmol scripts
using the javascripts was finally accomplished by making one large
pseudo NMR pdb file using many pdb files.  One script that
selected specific areas was applied when the nmrpdb file first loaded.
However, to toggle between two rasmol scripts, javascripts are not needed.
This can be done with the "altscript=" embed option (which does not appear
to be compatable with Chime 1.0).

Although there appears to be another problem which I hope can also be
answered.  When the "nmrpdb=true" embed option is loaded, external scripts
will not load with the "script="script test.scr"  The script file is in
the same directory and what's strange is the option "script="color red"
(or any other scripts written in) will work.  Thus the problem only
affects the script command! 
Any explainations??   

Dan Roseman
Emory University
Atlanta, GA

 mory.edu>
References: < <Pine.SGI.3.96.981109122651.25618A-100000@sneezey.bimcore.emory.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Tim Maffett <tim@mdli.com>
Subject: Re: toggling rasmol scripts
Date: Fri, 20 Nov 1998 15:00:52 -0800
To: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu

At 11:24 AM 11/20/98 -0500, Dan Roseman wrote:
>> 
>> Is there a way to use a single button (TYPE=submit) that would
>> cycle through multiple Rasmol/Chime scripts?  I've been able to toggle
>> between two scripts using one button based upon javascripts written by Dr.
>> Martz.  This most likely requires some javascripting as well.  Thanks.
>
>
>Thanks to some responses, I have some answers that one might be interested
>in knowing.  The problem of cycling through a series of Rasmol scripts
>using the javascripts was finally accomplished by making one large
>pseudo NMR pdb file using many pdb files.  One script that
>selected specific areas was applied when the nmrpdb file first loaded.
>However, to toggle between two rasmol scripts, javascripts are not needed.
>This can be done with the "altscript=" embed option (which does not appear
>to be compatable with Chime 1.0).
>
>Although there appears to be another problem which I hope can also be
>answered.  When the "nmrpdb=true" embed option is loaded, external scripts
>will not load with the "script="script test.scr"  The script file is in
>the same directory and what's strange is the option "script="color red"
>(or any other scripts written in) will work.  Thus the problem only
>affects the script command! 
>Any explainations??   

  This bug (loading scripts from disk in nmr mode) 
has been fixed in Chime 2.0 final release.  In addition the nmrpdb=
tag is no longer needed.

>
>
>
>Dan Roseman
>Emory University
>Atlanta, GA
>
>

++++------+------+------+------+------+------+------+------+------+------+
From: <A.R.C.Raine@bioc.cam.ac.uk>
Subject: Delivery of Rasmol scripts
Date: Mon, 23 Nov 1998 11:04:39 +0000 (GMT)
To: rasmol@dhcp-srv2.oit.umass.edu

Dear All,

I am a reasonably long-standing user of RasMol, but am new to scripts,
and to this email discussion group.  I have recently started to try and
assemble some supplementary information for my undergraduate students,
and I'd like to include rasmol scripts.  My first attempts can bee seen at:

http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/mvst1a_supp_mat.html

My real question is, though, what is the recomended way of delivering
this sort of information in the most general way?  My students will be
using PCs and Macs, but the method I have so far used (delivering the
scripts with coordinates in-line, and of MIME-type
application/x-rasmol) will only work properly for UNIX clients (as far
as I can tell!).

What should I be doing?  Recommending Chime?  Setting up the clients to
use RasMol (RasMac and RasWin) better?

I have read the documents at the UMass. site and at some others, but
everything seems to be dated about '96 - am I missing the up-to-date
documentation?

Thanks for your time,

Andrew

--
Dr. Andrew Raine, Department of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
Tel: +44 1223 333744,  FAX: +44 1223 766002, email: A.R.C.Raine@bioc.cam.ac.uk
WWW:http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/

References: <E0zhtnM-0002Xg-00@eden.bioc.cam.ac.uk>
++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: Re: Delivery of Rasmol scripts
Date: Mon, 23 Nov 1998 13:25:09 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

> My real question is, though, what is the recomended way of delivering
> this sort of information in the most general way?  My students will be
> using PCs and Macs, but the method I have so far used (delivering the
> scripts with coordinates in-line, and of MIME-type
> application/x-rasmol) will only work properly for UNIX clients (as far
> as I can tell!).

Scripts can be delivered to Mac. In the MIME configuration of the
browser, the File Type must be set to RSML. In Netscape 4.0x there is a
bug which doesn't allow you to select RSML directly if you've previously
set it for RasMol. Details of how to overcome this is in documentation
in the PDB. From your local PDB mirror, follow the  _Visualization_ 
link about 3/4 of the way down the home page, then the  _Configure your
WWW browser_  link at the top of the resulting page

e.g.  http://www2.ebi.ac.uk/pdb-docs/config.html

I don't know of any way to do it for RasWin, and when I asked a similar
question six months ago I got no reply.

> 
> What should I be doing?  Recommending Chime?  Setting up the clients to
> use RasMol (RasMac and RasWin) better?

You're probably better off using Chime if it's only ever going to be run
from Macs and PCs.

Kurt

-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +-972-8-9342614
Weizmann Institute of Science   Fax: +-972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Selecting/saving/viewing residues near an active site
Date: Sun, 22 Nov 1998 22:25:20 -0500
To: Kenward Vaughan <kaynjay@igalaxy.net>
Cc: edmolvis@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu

At 11/23/98, you wrote:
>Hi Eric!
>
>I am a professor at a community college in Bakersfield, CA, using Rasmol
>as my first modeling tool in my classes.  I would really like to do the
>following but don't see any reference as to how ...(it would **really**
>help my students in an extra credit project :)
>
>To model an active site:  Is it possible to select atoms within a certain
>distance of the ligand, and include the entire residues of said atoms?? 
>Picking atoms within, say, 5 angstroms would be a nice way to limit the
>residues which would show up if a larger value, such as 10 angstroms, was
>used.  Having this atom selection translate to its entire residue would be
>nice ...
>
>So far the only thing I know to do for this is a simple select within
>(10.0, ligand), and I get the unavoidable undesired residues (not close
>enough to be considered a part of the site) and fragments of residues.
>
>Appreciate any light you could shed on this!
>
>Dr. Kenward Vaughan
>Professor of Chemistry
>Bakersfield College
>Bakersfield, CA
>
>kvaughan@bc.cc.ca.us
>kaynjay@igalaxy.net

1. How about examining the result of 'restrict within(5., ligand)' (where
'ligand' is the group name of the ligand, usually a 3-letter code obtained
by clicking on the ligand) by clicking on the non-ligand atoms, and
manually constructing a script of this sort:

select ligand or 22,46,132-135
(where the numbers are residue sequence numbers for the contacting residues)
wireframe 0.3

You can view the resulting image, or if you wish 'save pdb filename' which
will save only the selected atoms.  Then when you reload this new smaller
PDB file, rotating will work better at a high zoom because you don't have a
large structure filling RasMol's boundary limits.

2. Alternatively, you could use my Noncovalent Bond Finder at

www.umass.edu/microbio/chime/find-ncb
which automatically finds the atoms closest to the ligand (by clicking on
Find), then you can pick 'Show entire residue, CPK coloring' from the
mouse-clicks menu, and when you click on the closest atom, the entire
residue is filled out.  This allows the students to focus on the content
rather than the technology, by making it much easier to see the close
residues.
(At high zoom, rotation may push the ligand off-screen due to the boundary
limits.  Therefore here too it may help to first save the relevant portion
of the complex from RasMol as in #1 above. N.B. Chime can save PDB files
but it always saves the entire file, not the selected subset like RasMol.
Details are at www.umass.edu/microbio/rasmol/pdbtools.htm)

3. You may wish to have a look at Manfred Hendlich's ReliBase.  This is a
database of all ligands in the PDB, allowing you to search by ligand or
substructure.  When you select a ligand in a particular PDB file, one
option is to view the 'active site' in a Chime viewer I constructed
especially to show just the ligand and atoms within 7 Angstroms of it. You
get to ReliBase at the PDB (www.pdb.bnl.gov) under Other Search Tools. The
ReliBase URL is:

http://www.pdb.bnl.gov:8081/home.html

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Delivery of Rasmol scripts
Date: Mon, 23 Nov 1998 10:35:57 -0500
To: <A.R.C.Raine@bioc.cam.ac.uk>
Cc: rasmol@dhcp-srv2.oit.umass.edu

In my opinion you should be recommend/using Chime to deliver the scripts.
RasMol development stopped in 1996 (tho we continue to update the
documentation when we spot needs).
The newest items, and most active area at my site is the Chime section.
Use the downloadable Chime template which means you and your students don't
have to learn javascript or much html to make a slick presentation. In
workshops, once people understand how to use RasMol and save scripts, the
presentation of the saved scripts in Chime can be taught in a single
afternoon. The template and step by step documentation are at

www.umass.edu/microbio/chime/prsswc

At 11/23/98, you wrote:
>Dear All,
>
>I am a reasonably long-standing user of RasMol, but am new to scripts,
>and to this email discussion group.  I have recently started to try and
>assemble some supplementary information for my undergraduate students,
>and I'd like to include rasmol scripts.  My first attempts can bee seen at:
>
>http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/mvst1a_supp_mat.html
>
>My real question is, though, what is the recomended way of delivering
>this sort of information in the most general way?  My students will be
>using PCs and Macs, but the method I have so far used (delivering the
>scripts with coordinates in-line, and of MIME-type
>application/x-rasmol) will only work properly for UNIX clients (as far
>as I can tell!).
>
>What should I be doing?  Recommending Chime?  Setting up the clients to
>use RasMol (RasMac and RasWin) better?
>
>I have read the documents at the UMass. site and at some others, but
>everything seems to be dated about '96 - am I missing the up-to-date
>documentation?
>
>Thanks for your time,
>
>Andrew
>
>--
>Dr. Andrew Raine, Department of Biochemistry, University of Cambridge,
>80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
>Tel: +44 1223 333744,  FAX: +44 1223 766002, email:
A.R.C.Raine@bioc.cam.ac.uk
>WWW:http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/
> 
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <3658EFC7.F38E26BD@igalaxy.net>
++++------+------+------+------+------+------+------+------+------+------+
From: Gale Rhodes <rhodes@usm.maine.edu>
Subject: Re: Selecting/saving/viewing residues near an active site
Date: Mon, 23 Nov 1998 15:52:30 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Selection of whole residues as neighbors to the current selection occurs as
the default in SwissPDbViewer. SPdbV also shows all or none of each
residues during slabbing operations, which is especially nice in stereo,
because both stereo views always have exactly the same content. Slabbing in
stereo in RasMol or Chime often produces uncomfortable disparities between
the two views.

Cheers!

>At 11/23/98, you wrote:
>>Hi Eric!
>>
>>I am a professor at a community college in Bakersfield, CA, using Rasmol
>>as my first modeling tool in my classes.  I would really like to do the
>>following but don't see any reference as to how ...(it would **really**
>>help my students in an extra credit project :)
>>
>>To model an active site:  Is it possible to select atoms within a certain
>>distance of the ligand, and include the entire residues of said atoms??
>>Picking atoms within, say, 5 angstroms would be a nice way to limit the
>>residues which would show up if a larger value, such as 10 angstroms, was
>>used.  Having this atom selection translate to its entire residue would be
>>nice ...
>>
>>So far the only thing I know to do for this is a simple select within
>>(10.0, ligand), and I get the unavoidable undesired residues (not close
>>enough to be considered a part of the site) and fragments of residues.
>>
>>Appreciate any light you could shed on this!
>>
>>Dr. Kenward Vaughan
>>Professor of Chemistry
>>Bakersfield College
>>Bakersfield, CA
>>
>>kvaughan@bc.cc.ca.us
>>kaynjay@igalaxy.net
>
>1. How about examining the result of 'restrict within(5., ligand)' (where
>'ligand' is the group name of the ligand, usually a 3-letter code obtained
>by clicking on the ligand) by clicking on the non-ligand atoms, and
>manually constructing a script of this sort:
>
>select ligand or 22,46,132-135
>(where the numbers are residue sequence numbers for the contacting residues)
>wireframe 0.3
>
>You can view the resulting image, or if you wish 'save pdb filename' which
>will save only the selected atoms.  Then when you reload this new smaller
>PDB file, rotating will work better at a high zoom because you don't have a
>large structure filling RasMol's boundary limits.
>
>2. Alternatively, you could use my Noncovalent Bond Finder at
>
>www.umass.edu/microbio/chime/find-ncb
>which automatically finds the atoms closest to the ligand (by clicking on
>Find), then you can pick 'Show entire residue, CPK coloring' from the
>mouse-clicks menu, and when you click on the closest atom, the entire
>residue is filled out.  This allows the students to focus on the content
>rather than the technology, by making it much easier to see the close
>residues.
>(At high zoom, rotation may push the ligand off-screen due to the boundary
>limits.  Therefore here too it may help to first save the relevant portion
>of the complex from RasMol as in #1 above. N.B. Chime can save PDB files
>but it always saves the entire file, not the selected subset like RasMol.
>Details are at www.umass.edu/microbio/rasmol/pdbtools.htm)
>
>3. You may wish to have a look at Manfred Hendlich's ReliBase.  This is a
>database of all ligands in the PDB, allowing you to search by ligand or
>substructure.  When you select a ligand in a particular PDB file, one
>option is to view the 'active site' in a Chime viewer I constructed
>especially to show just the ligand and atoms within 7 Angstroms of it. You
>get to ReliBase at the PDB (www.pdb.bnl.gov) under Other Search Tools. The
>ReliBase URL is:
>
>http://www.pdb.bnl.gov:8081/home.html
>
>
>/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
>Eric Martz, Professor (Immunology), Dept Microbiology
>Morrill IVN 203, U Mass, Amherst MA US 01003-5720
>413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu
>
>Molecular visualization in bioscience education at the
>RasMol Home Page <http://www.umass.edu/microbio/rasmol>
>- - - - - - - - - - - - - - - - - - - - - - - - - - - */

*****************************

Gale Rhodes   mailto:rhodes@usm.maine.edu
http://macweb.acs.usm.maine.edu/chemistry/GR/GRHomePage.html
Professor of Chemistry
Chemistry Department
University of Southern Maine
PO Box 9300
Portland, Maine 04104-9300
Phone: (207)780-4734 (W)
Fax:   (207)780-5607 (W)

++++------+------+------+------+------+------+------+------+------+------+
From: <A.R.C.Raine@bioc.cam.ac.uk>
Subject: Re: Delivery of Rasmol scripts
Date: Wed, 25 Nov 1998 10:47:29 +0000 (GMT)
To: rasmol@dhcp-srv2.oit.umass.edu

Thanks to all who replied to my question about delivery of RasMol
scripts to students via the WWW.  I will try the strategies suggested
and get back to you all if I still have problems!

Andrew

--
Dr. Andrew Raine, Department of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
Tel: +44 1223 333744,  FAX: +44 1223 766002, email: A.R.C.Raine@bioc.cam.ac.uk
WWW:http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/

++++------+------+------+------+------+------+------+------+------+------+
From: "Brendan O'Malley" <BRENDAN@bunyip.ph.rmit.edu.au>
Subject: Chime and SGI's
Date: Thu, 26 Nov 1998 09:37:16 EST-10ESUT
To: rasmol@dhcp-srv2.oit.umass.edu

I'd like to put chime scripts on my web page, but our server is an 
SGI Indy runing IRIX 6.5. Will any version of chime run on this? I've 
installed the chime0.9z version and am using Netscape Communicator 
but I find I just get a 'download plugin' message when I load a local 
or external web page with chime material. Thanks in advance for any 
help

Brendan O'Malley
Applied Physics
RMIT

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Chime and SGI's
Date: Wed, 25 Nov 1998 18:08:37 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

At 11/26/98, you wrote:
>I'd like to put chime scripts on my web page, but our server is an 
>SGI Indy runing IRIX 6.5. Will any version of chime run on this? I've 
>installed the chime0.9z version and am using Netscape Communicator 
>but I find I just get a 'download plugin' message when I load a local 
>or external web page with chime material. Thanks in advance for any 
>help
>
>Brendan O'Malley
>Applied Physics
>RMIT
> 

Chime 0.9 is the only version available for SGI.  It should work on some
Chime pages, e.g. the viewer at the end of PDB Lite (www.pdb.bnl.gov) when
you complete a search and select one molecule for viewing (click on the
Chemscape Chime link under viewing).

You need to configure the MIME types for your SGI in order to make it work.
 The types are .pdb to chemical/x-pdb, .spt to application/x-spt, and .js
to application/x-javascript. I don't the details for SGI, perhaps another
subscriber to this list can help?

The complete list is at http://www.mdli.com/support/chime/faq_install.html

Obviously sites requiring Chime 1 or 2 won't work on an SGI.  I develop
everything on Windows (Mac would also be fine now that Chime 2 is out for
it) and then put it on the server. The server doesn't need to run Chime in
order to serve Chime resources.  I view them on my Windows machine from the
server.

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

	charset="iso-8859-1"
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++++------+------+------+------+------+------+------+------+------+------+
From: "Yi He" <yhe0@pop.uky.edu>
Subject: how to use PDB file in MS Office?
Date: Sat, 28 Nov 1998 00:04:05 -0500
To: <rasmol@dhcp-srv2.oit.umass.edu>

Hi, Dear Rasmolians:

I am going to give a presentation about nucleic acids and other bio-molecules. Does anyone know how to incorporate PDB files into the Microsoft PowerPoint slides? I know I can export the PDB files as images and load them upto PowerPoint, but I wonder if I can embed them as objects and be able to manipulate them during the slide show.

Thanks a lot.

Yi

References: <004501be1a8c$9c23fb60$f370fed0@yeeho>
++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: Re: how to use PDB file in MS Office?
Date: Sat, 28 Nov 1998 11:49:23 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

Yi He wrote:
> 
> Hi, Dear Rasmolians:
> 
> I am going to give a presentation about nucleic acids and other bio-molecules. Does anyone know how to incorporate PDB files into the Microsoft PowerPoint slides? I know I can export the PDB files as images and load them upto PowerPoint, but I wonder if I can embed them as objects and be able to manipulate them during the slide show.
> 

I haven't tried it, but the WebLab viewer from MSI
(http://www.msi.com/weblab/) claims to be "OLE compatible" so you can
embed it in documents. A free version (WebLab viewer Lite) is available.

I'm sure many on the list (myself included) would be interested to know
how it comes out.

Kurt

-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +-972-8-9342614
Weizmann Institute of Science   Fax: +-972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

	charset="koi8-r"
X-MSMail-Priority: Normal
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++++------+------+------+------+------+------+------+------+------+------+
From: "Sergey Vasil'ev" <vasil@iab.ac.ru>
Subject: Save structure parameters from RasMol
Date: Sat, 28 Nov 1998 18:27:22 +0300
To: <rasmol@dhcp-srv2.oit.umass.edu>

Hi All!

When RasMol works with PDB file without header or when you use command
<structure> RasMol calculates secondary structure of protein by itself.

Q: Is it possible to save information about protein structure  after using
command <structure> in PDB header or any other way?

Thank you very much in advance.

Sergey Vasil'ev
----------------------------------------------------------------------
BioComputing Group,                 | tel.   +7-095-9760560
Inst. of Agricultural BioTechnology,| fax.   +7-095-9770947
42 Timiryazevskaya St.,             | email  vasil@yann.genebee.msu.su
Moscow 127550, RUSSIA               |        vasil@iab.ac.ru

++++------+------+------+------+------+------+------+------+------+------+
From: Timothy Pickering <timp@vt.edu>
Subject: Problem with Chime2.0 Installation
Date: Sat, 28 Nov 1998 10:56:11 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Hope someone can offer some suggestions for the following problem.  Anyone
else experienced anything like this? 

Tried to install the Chime2.0 plug in from MDLI but it bombed my system.
Here is what I did.

Downloaded the Win95 version of Chime2.0 from the MDLI web site.  

Turned off anti-virus protection and restarted the computer.  Double
clicked on the ch20w32 icon in the Netscape folder.  

Got a dialog box with no text displayed and the error alert sound.  When I
closed the dialog box, my computer restarted, and when it came it up I got
the Improper Shut down error message.  Had to use CNTL-ALT-DEL to get
restarted.

I have Internet Explorer 4.01 as my default browser, but want to install
this plug-in for the Netscape browser, which is also installed.  I am
running Navigator 4.05.  Sure is a mess. 

System details.  Micron Millennium computer, Pentium 166 processor, 32 Mb
RAM, Win95 OSR2.

Tim Pickering
Virginia Tech

References: <001201be1ae3$97fe8210$611c22c3@sergey>
++++------+------+------+------+------+------+------+------+------+------+
From: Kurt Giles <kurt@inn-prot.weizmann.ac.il>
Subject: Re: Save structure parameters from RasMol
Date: Sat, 28 Nov 1998 18:42:26 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

> When RasMol works with PDB file without header or when you use command
> <structure> RasMol calculates secondary structure of protein by itself.
> 
> Q: Is it possible to save information about protein structure  after using
> command <structure> in PDB header or any other way?
> 

I don't know if it's possible to get it diretcly through RasMol. But
RasMol just uses DSSP, which you can get for various platforms from
http://www.sander.embl-heidelberg.de/dssp/

Kurt
-- 
---------------------------------------------------------------
Dr. Kurt Giles                  kurt@inn-prot.weizmann.ac.il 
Israeli National Node           
Biological Computing Unit       Tel: +972-8-9342614
Weizmann Institute of Science   Fax: +972-8-9466269
Rehovot 76100, Israel           http://inn-prot.weizmann.ac.il/
---------------------------------------------------------------

References: <004501be1a8c$9c23fb60$f370fed0@yeeho>
 boundary="------------B696CC43013D222F9C5BF3BB"
X-Accept-Language: en
++++------+------+------+------+------+------+------+------+------+------+
From: "John J. Stezowski" <jjs@unlinfo.unl.edu>
Subject: Re: how to use PDB file in MS Office?
Date: Sat, 28 Nov 1998 10:59:23 -0600
To: rasmol@dhcp-srv2.oit.umass.edu

This is a multi-part message in MIME format.
--------------B696CC43013D222F9C5BF3BB

Hi,
I simply link a PDB file in powerpoint.  When called it opens my browser and used the Chime plugin. This assume you have a browser on the computer you are running the powerpoint slide show from.
JJS

Yi He wrote:

> Hi, Dear Rasmolians:
>
> I am going to give a presentation about nucleic acids and other bio-molecules. Does anyone know how to incorporate PDB files into the Microsoft PowerPoint slides? I know I can export the PDB files as images and load them upto PowerPoint, but I wonder if I can embed them as objects and be able to manipulate them during the slide show.
>
> Thanks a lot.
>
> Yi

--------------B696CC43013D222F9C5BF3BB
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version:2.1
email;internet:jjs@unlinfo.unl.ecu
fn:John J. Stezowski
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--------------B696CC43013D222F9C5BF3BB--

	boundary="----_=_NextPart_001_01BE1E30.AE334854"
++++------+------+------+------+------+------+------+------+------+------+
From: Morgan Ryan <mryan@worthpub.com>
Subject: 2.0a for Mac is ... here?
Date: Wed, 2 Dec 1998 15:21:39 -0500 
To: "'rasmol@dhcp-srv2.oit.umass.edu'" <rasmol@dhcp-srv2.oit.umass.edu>

This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

------_=_NextPart_001_01BE1E30.AE334854

The Chime website says that 2.0a for Mac is available, but the link doesn't
work:

http://www.mdli.com/download/chime/Chime_2.0a_Installer.sit

The release notes say that the slow script problem is fixed (!). Has anyone
gotten it? Morgan Ryan

----------------
Morgan Ryan
Development Editor
Worth Publishers
33 Irving Place
New York, NY 10003
212-475-6000
mryan@worthpub.com

------_=_NextPart_001_01BE1E30.AE334854

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Dus-ascii">
<META NAME=3D"Generator" CONTENT=3D"MS Exchange Server version =
5.5.2232.0">
<TITLE>2.0a for Mac is ... here?</TITLE>
</HEAD>
<BODY>

<P><FONT FACE=3D"Arial">The Chime website says that 2.0a for Mac is =
available, but the link doesn't work:</FONT>
</P>

<P><FONT FACE=3D"Arial"><A =
HREF=3D"http://www.mdli.com/download/chime/Chime_2.0a_Installer.sit" =
TARGET=3D"_blank">http://www.mdli.com/download/chime/Chime_2.0a_Installe=
r.sit</A></FONT>
</P>

<P><FONT FACE=3D"Arial">The release notes say that the slow script =
problem is fixed (!). Has anyone gotten it? Morgan Ryan</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Geneva">----------------</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Geneva">Morgan Ryan</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Geneva">Development Editor</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Geneva">Worth Publishers</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Geneva">33 Irving Place</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Geneva">New York, NY 10003</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Geneva">212-475-6000</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Geneva">mryan@worthpub.com</FONT>
</P>

</BODY>
</HTML>
------_=_NextPart_001_01BE1E30.AE334854--

++++------+------+------+------+------+------+------+------+------+------+
From: timp@vt.edu (Timothy L. Pickering)
Subject: Re: 2.0a for Mac is ... here?
Date: Thu, 3 Dec 1998 08:26:33 -0400
To: rasmol@dhcp-srv2.oit.umass.edu

Morgan Ryan wrote:

>The Chime website says that 2.0a for Mac is available, but the link doesn't
>work:
>
>http://www.mdli.com/download/chime/Chime_2.0a_Installer.sit
>
>The release notes say that the slow script problem is fixed (!). Has anyone
>gotten it? Morgan Ryan
>

MDL seems to be having some difficulty with their installer software.  I
wrote about this problem last week as follows:
================
Hope someone can offer some suggestions for the following problem.  Anyone
else experienced anything like this?

Tried to install the Chime2.0 plug in from MDL but it bombed my system.
Here is what I did.

Downloaded the Win95 version of Chime2.0 from the MDLI web site.

Turned off anti-virus protection and restarted the computer.  Double
clicked on the ch20w32 icon in the Netscape folder.

Got a dialog box with no text displayed and the error alert sound.  When I
closed the dialog box, my computer restarted, and when it came it up I got
the Improper Shut down error message.  Had to use CNTL-ALT-DEL to get
restarted.
===========
I left a note for MDL tech support and received a call from them within a
day or two.  The explanation was that the installer software was not
working properly.  They left a copy of the new installer for me at an ftp
site (too big to E-mail).  I downloaded that file and it worked fine.  My
solution won't help you because you need the Mac version.  Sounds like
there is a similar problem with the installer for the Mac.  Based on my
experience, I would suggest leaving a note for MDL tech support on their
web page.

Tim Pickering
Virginia Tech

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Chime 2.0a for the Macintosh
Date: Thu, 03 Dec 1998 13:24:27 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

I was able to start the download of Chime 2.0a for the Macintosh from
http://www.mdli.com/support/chime/download.html (but I didn't finish it
since I am using Windows). MDLI's site indicates that it was released
12/1/98. I hope a Mac user familiar with the timing problems in Chime 2.0
for the Mac will soon let us know how 2.0a behaves!

-Eric

- - - 
Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US 01003-5720

RasMol Email List <www.umass.edu/microbio/rasmol/raslist.htm>

References: <199812031820.NAA23840@marlin.bio.umass.edu>
 x-mac-creator="4D4F5353"
++++------+------+------+------+------+------+------+------+------+------+
From: Tim <tdriscol@unix.amherst.edu>
Subject: Re: Chime 2.0a for the Macintosh
Date: Thu, 03 Dec 1998 14:20:45 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Eric Martz wrote:

> I was able to start the download of Chime 2.0a for the Macintosh from
> http://www.mdli.com/support/chime/download.html (but I didn't finish it
> since I am using Windows). MDLI's site indicates that it was released
> 12/1/98. I hope a Mac user familiar with the timing problems in Chime 2.0
> for the Mac will soon let us know how 2.0a behaves!
>
> -Eric
>
> - - -
> Eric Martz, Professor (Immunology), Dept Microbiology
> U Mass, Amherst MA US 01003-5720
>
> RasMol Email List <www.umass.edu/microbio/rasmol/raslist.htm>

I just installed Chime 2.0a on my Mac and it works great!  The download and
installation were smooth (I already had Chime 1.0 installed), and the
timing/delay bug seems to be _mostly_ worked out.  The delays were still
longer in 2.0a than in 1.0, but much more manageable (i.e., only about twice
as long).

I'm using a 180 MHz PowerComputing machine with 80 MB RAM running OS 8.1 and
Communicator 4.5 (20 MB RAM allocated).

Tim Driscoll
UMass Amherst
Molecular and Cellular Biology Program

X-MSMail-Priority: Normal
++++------+------+------+------+------+------+------+------+------+------+
From: "Van de Wiele Annie" <avandewiele@nordnet.fr>
Subject: image bmp with Rasmol
Date: Tue, 8 Dec 1998 10:52:40 +0100
To: "rasmol lists" <rasmol@dhcp-srv2.oit.umass.edu>

To Rasmol Users

Thanks to all for giving some help to a beginner who would want to make
images bmp with a script.
I use the  command "export", I make a file "name".bmp but when I click on
the file my PC says:
<<"name".bmp unobtainable, memory not suffisant to create the image>>

But I have yet 258 MO free on the disc
My PC is a pentium 233 MMX, 64 mega with windows 95, and Coreldraw
photopaint takes always the hand when I want to make image bmp ?

Kind regards.

Annie

avandewiele@nordnet.fr

   

++++------+------+------+------+------+------+------+------+------+------+
From: Shannon Qualie <shannon.qualie@ualberta.ca>
Subject: Chime Animations
Date: Thu, 10 Dec 1998 16:27:20 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

Hi,
I am new to this list so please forgive me if I delve into previously
covered territory.
I am attempting to use Chime and RasMol to make animations of simple
chemical reactions for professors.  I am would like to do the animations in
.XYZ format so that I can do away with long RasMol scripts. I am using a
commercial program (ChemSite by Pyramid Learning) to create the molecules
and save them as MDL molfiles. When I load the molecules into RasMol and
convert them to pdb format (using the save pdb filename.pdb command) they
go very strange.  Some atoms have bonds all over the place that weren't
there before and others suddenly have no bonds at all. 
I have hand written an XYZ animation of two atoms approaching each other. I
 expected that a bond would appear at some point but the atoms behave as
independent entities even when they mash together. I built a tetrahedral
molecule in ChemSite and used the coordinates it found to write a RasMol
script where a water molecule approaches it.  I have hydrogens bonding to 3
and 4 things at once without my specification. This does not appear to be a
factor of distance because atoms that are farther apart will have a bond
while closer atoms will be bondless. I know a picture is worth a thousand
words so I have put these "failures" up on a server at:

		http://www.chem.ualberta.ca/~squalie/script/NEXT.html

These animations are very nearly first drafts so forgive their jerkiness
please.
Now for the actual questions:
1. Does RasMol usually do strange things when converting from .mol to .pdb?
2. Am I missing something in my handwritten XYZ files?
3. Do any of you use programs to create the images that you need in your
scripts, or do you do it all manually?
4. Are there any programs (free?) for building molecules that can save in
both .pdb and .XYZ format?

Shannon Qualie
Industrial Intern 1998/1999
Department of Chemistry
University of Alberta
Edmonton, Canada
shannon.qualie@ualberta.ca

++++------+------+------+------+------+------+------+------+------+------+
From: Jens Grabenstein <Jens.Grabenstein@surf24.de>
Subject: Chime MIME Server Setup
Date: Sat, 12 Dec 1998 15:17:41 +0100
To: <rasmol@dhcp-srv2.oit.umass.edu>

Hello,

I am using Chime for a web-based tutorial. Everything works fine on the 
local hard disk, but after uploading the tutorial to our server, it 
doesn't work. Sometimes, you just get a missing plug-in page, but more 
often Chime is loaded, however no molecule is displayed even though the 
pdb-file has been loaded (at least "loading pdb-file" is displayed in the 
status bar). By clicking on the page the Chime pop-up menu appears, but 
no option is available. I think the problem is that we need to change the 
server's MIME settings. But after changing the settings the problem still 
exists. Does anybody know the reason?

Thanks in advance

Jens Grabenstein

----------------------------------
Jens Grabenstein
University of Konstanz
Faculty of Biology
Jens.Grabenstein@uni-konstanz.de
----------------------------------

++++------+------+------+------+------+------+------+------+------+------+
From: Harry Ungar <haungar@cruzio.com>
Subject: Re: Chime 2.0a for the Macintosh
Date: Sat, 12 Dec 1998 09:05:14 -0700
To: <rasmol@dhcp-srv2.oit.umass.edu>

Without any difficulty, I have recently downloaded and  installed and 
quickly tested Chime 2.0a for the Mac using Netscape Navigator 4.05.

It definitely made scripts with move commands (which caused timing 
problems in the previous version) work much better. But they still seem 
to be a little slower than with the PC version.

Harry

>I was able to start the download of Chime 2.0a for the Macintosh from
>http://www.mdli.com/support/chime/download.html (but I didn't finish it
>since I am using Windows). MDLI's site indicates that it was released
>12/1/98. I hope a Mac user familiar with the timing problems in Chime 2.0
>for the Mac will soon let us know how 2.0a behaves!
>
>-Eric
>
>- - - 
>Eric Martz, Professor (Immunology), Dept Microbiology
>U Mass, Amherst MA US 01003-5720
>
>RasMol Email List <www.umass.edu/microbio/rasmol/raslist.htm>
>
>

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Molecular Christmas Tree
Date: Sun, 13 Dec 1998 15:55:49 -0500
To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu
Cc: pdb-l@pdb.pdb.bnl.gov

Gale Rhodes has created a wonderful molecular christmas tree (made from
adipocyte lipid binding protein, 1ALB) and at my request, kindly given his
permission for us to decorate the RasMol Home Page with it for the season.
Take a look at http://www.umass.edu/microbio/rasmol

I am hoping other enterprising artists will be inspired to provide a
molecular menorah and other seasonal molecular art representing other
cultures!  Perhaps a modified topology diagram from a seven-span
transmembrane protein? 

Season's greetings,
-Eric Martz

P.S. If you see the old immunoglobulin domain masthead instead of the
christmas tree, press the Reload button on your browser!

++++------+------+------+------+------+------+------+------+------+------+
From: "I.Smirnov" <ivsmirn@itsa.ucsf.edu>
Subject: MEP surface coloring in Chime2?
Date: Wed, 16 Dec 1998 10:15:57 -0800 (PST)
To: rasmol@dhcp-srv2.oit.umass.edu

Question to Chime gurus:

I am trying to color the surface of DNA (in PDB format) by electrostatic
potential in Chime 2. Though it works just fine with the proteins,
it doesn't with the DNA. I tried different options (mep
function/mode/distance) with no success.
What am I missing?
Or this feature is limited to proteins only?

Thanx in advance.
-------------------------------
Dr. Ivan Smirnov
Dept.Pharm.Chem.
UCSF, CA, USA

++++------+------+------+------+------+------+------+------+------+------+
From: Dan Roseman <drose07@sneezey.bimcore.emory.edu>
Subject: Re: Chime MIME Server Setup
Date: Wed, 16 Dec 1998 17:22:08 -0500 (EST)
To: rasmol@dhcp-srv2.oit.umass.edu

Hello Jens,

If a web page works locally, then there should be no problem once the code
is on the server as long as everything is the same.  In other words, when
you viewed the page on the server, was it the same page you were looking
at locally (I often keep different backup copies), were you on the same
computer?  Changing the MIME type on the server doesn't really matter.
This is probably something very small.  I once had many of my files
locally in upper case, and when I sent them to the server, the case was
lowered.  Thus, the HTML didn't know where my file was!  Another problem
might be file location.  You should make sure the HTML is not pointing to
the pdb file on your local computer.  Hope this helps.
Good luck,
-Dan Roseman

On Sat, 12 Dec 1998, Jens Grabenstein wrote:

> Hello,
> 
> I am using Chime for a web-based tutorial. Everything works fine on the 
> local hard disk, but after uploading the tutorial to our server, it 
> doesn't work. Sometimes, you just get a missing plug-in page, but more 
> often Chime is loaded, however no molecule is displayed even though the 
> pdb-file has been loaded (at least "loading pdb-file" is displayed in the 
> status bar). By clicking on the page the Chime pop-up menu appears, but 
> no option is available. I think the problem is that we need to change the 
> server's MIME settings. But after changing the settings the problem still 
> exists. Does anybody know the reason?
> 
> Thanks in advance
> 
> Jens Grabenstein
> 
> ----------------------------------
> Jens Grabenstein
> University of Konstanz
> Faculty of Biology
> Jens.Grabenstein@uni-konstanz.de
> ----------------------------------
> 

++++------+------+------+------+------+------+------+------+------+------+
From: "Fernando Gabriel Ranea  " <fgranea@microb.ffyb.uba.ar>
Subject: XYZ animated
Date: Tue, 15 Dec 1998 00:39:57 ARG
To: rasmol@dhcp-srv2.oit.umass.edu

Hi!

Where I can find information, like a short tutorial or guide, for build a
XYZ animated file and use it with the Chime.
Sincerely,

Fernando Gabriel Ranea 
fgranea@microb.ffyb.uba.ar

References: <366027F2.CAF33110@inn-prot.weizmann.ac.il>
++++------+------+------+------+------+------+------+------+------+------+
From: Shannon Qualie <shannon.qualie@ualberta.ca>
Subject: Re: XYZ animated
Date: Wed, 16 Dec 1998 17:19:03 -0700
To: rasmol@dhcp-srv2.oit.umass.edu

>Where I can find information, like a short tutorial or guide, for build a
>XYZ animated file and use it with the Chime.
These are all the sites I find that I have to return to frequently. The
first on is my favorite. I too am a beginner at this  but if I can help in
any way feel free to contact me. The ones with stars (**) are the most
helpful, if you don't mind sifting through the enormous amount of
information. : )

Enhanced web document with Chime **
		http://www.chem.niu.edu/IJC/Text/chime.html

Chime Primer- there to help you
     	http://www.mdli.com/support/chime/primer.htm 

How To Make Chime/RasMol Presentations **
     	http://www.umass.edu/microbio/rasmol/maketuts.htm 

MDL Worldwide Services: Chime Embed Tags and Scripting Reference
    		http://www.mdli.com/support/chime/embed.htm

MDL Worldwide Services: Chime Free Support
            http://www.mdli.com/support/chime/chimefree.htm

MDL Worldwide Services: Chime Sample Sites
   		http://www.mdli.com/support/chime/cool.htm

Good Luck !

Shannon Qualie
Industrial Intern 1998/1999
Department of Chemistry
University of Alberta
Edmonton, Canada
shannon.qualie@ualberta.ca

X-Accept-Language: en
++++------+------+------+------+------+------+------+------+------+------+
From: Sorin Pancotan <pancotan@geocities.com>
Subject: Double bonds ,3D glasses
Date: Thu, 17 Dec 1998 13:44:55 +0200
To: rasmol@dhcp-srv2.oit.umass.edu

    Hi !

    My first question is :
    -How can i visualize double bonds (-HC=CH-) in RasMol and Chime ?
I've read the entire RasMol manual ,and i did not find a word  about it
.In Chime i've find
the option "Display wireframe double bonds" but is inactive with every
molecule i've tried .It must be a record in the PDB file ?

    The second question is :
    -What kind of glasses or goggles have to use to see in 3D the
molecules in "3D mode" ?
Can i find something about it on the Net? Or buy it somewhere?

P.S.   I'm using RasWin 2.6 and Chime 2.0

    Thanks in advance

References: <3678EEB7.BF138181@geocities.com>
++++------+------+------+------+------+------+------+------+------+------+
From: Sonia Quaratino <S.Quaratino@s1.cxwms.ac.uk>
Subject: plug-in
Date: Thu, 17 Dec 1998 12:31:24 +0000
To: rasmol@dhcp-srv2.oit.umass.edu

Hi all,
I am new to the area, I downloaded Chime and was asked for the plug-in
chemical/x-xyz. However, cannot manage to download this plug-in.  Any
suggestion?
thanks in advance
sonia

++++------+------+------+------+------+------+------+------+------+------+
From: Gale Rhodes <rhodes@usm.maine.edu>
Subject: Seeing 3D in Stereo Pairs
Date: Thu, 17 Dec 1998 07:58:21 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Most people can train themselves to cross or diverge their eyes and see 3D
with stereo pairs in RasMol, SwissPdbViewer or other such programs. For
training, see this web page:

http://macweb.acs.usm.maine.edu/chemistry/GR/0Help/StereoView.html

That's "zeroHelp" between the last two slashes.

Also, a company called nu3Dvu makes goggles containing a system of mirrors
that allows you to converge 3D pairs if you can't teach your eyes to do it.
They are somewhat bulky and awkward, and when wearing them, you must close
one eye to see menus, your keyboard, or your sandwich. According to
AltaVista, nu3Dvu is at

http://www.nu3dvu.com

but I can't connect with them this morning.

For more information about nu3Dvu viewers, see

http://uwmml.pharmacy.wisc.edu/nu3Dvu.html

All kinds of 3D viewing and design tools are available at Reel 3D Enterprises:

http://www.stereoscopy.com/reel3d/

It makes me happy when I learn that people are trying to use stereo pairs.
You don't know what you're missing in big molecules until you explore them
in stereo. It's not just a gadget, it's a powerful tool. It's a little
uncomfortable at first, but good exercise for your eyes.

A couple of my students, a bit skeptical at first about stereo viewing,
gave me a mug with a stereo pair and a logo that says, "Crystallographers
do it cross-eyed." However, both of them learned to see stereo pairs in 3D.

Cheers!

*****************************

Gale Rhodes   mailto:rhodes@usm.maine.edu
http://macweb.acs.usm.maine.edu/chemistry/GR/GRHomePage.html
Professor of Chemistry
Chemistry Department
University of Southern Maine
PO Box 9300
Portland, Maine 04104-9300
Phone: (207)780-4734 (W)
Fax:   (207)780-5607 (W)

++++------+------+------+------+------+------+------+------+------+------+
From: "Patrick Flash" <flash@ashtabula.kent.edu>
Subject: Re: Double bonds ,3D glasses
Date: Thu, 17 Dec 1998 11:38:51 EST 
To: rasmol@dhcp-srv2.oit.umass.edu

Sorin,
    I'm currently working on an attempt to show red-blue anaglyphs 
(sp? not in my dictionary) using Rasmol.  I export a red and a blue 
copy of the Rasmol  images rotated + and - three degrees respectively 
in  BMP form.  Then I use Adobe Photo Delux  to overlay the images in 
one file.  In a Power Point presentation with red-blue goggles you 
get a true stereo effect.  So far I've only tried one molecule, ATP.  
The rings look great but the phosphate chain "ghosts" and I see two 
images.   Try http://yip5.chem.wfu.edu/yip/3D/3Dviewing.html for more 
directions.  I think many chem supply outfits carry the red-blue 
cardboard goggles.

Patrick Flash
Kent-Ashtabula  flash@ashtabula.kent.edu

++++------+------+------+------+------+------+------+------+------+------+
From: Harry Ungar <haungar@cruzio.com>
Subject: Re: Double bonds ,3D glasses
Date: Thu, 17 Dec 1998 09:16:39 -0700
To: <rasmol@dhcp-srv2.oit.umass.edu>

Chime will display double and triple bonds from a molecule file in the 
MDL Molfile format; the extension is .mol. All of the small molecules 
available from our Molecular Library  (http://c4.cabrillo.cc.ca.us) are 
in that format.

Pdb files do not contain double bond information. You can add them to a 
pdb file by hand coding each one. Directions for doing that are  at Eric 
Martz' site at UMass.

>    Hi !
>
>    My first question is :
>    -How can i visualize double bonds (-HC=CH-) in RasMol and Chime ?
>I've read the entire RasMol manual ,and i did not find a word  about it
>.In Chime i've find
>the option "Display wireframe double bonds" but is inactive with every
>molecule i've tried .It must be a record in the PDB file ?
>
>    The second question is :
>    -What kind of glasses or goggles have to use to see in 3D the
>molecules in "3D mode" ?
>Can i find something about it on the Net? Or buy it somewhere?
>
>P.S.   I'm using RasWin 2.6 and Chime 2.0
>
>    Thanks in advance
>
>

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: Double bonds ,3D glasses
Date: Thu, 17 Dec 1998 16:33:35 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

At 12/17/98, Sorin Pancotan <pancotan@geocities.com> wrote:
>    My first question is :
>    -How can i visualize double bonds (-HC=CH-) in RasMol and Chime ?
>I've read the entire RasMol manual ,and i did not find a word  about it
>.In Chime i've find
>the option "Display wireframe double bonds" but is inactive with every
>molecule i've tried .It must be a record in the PDB file ?

The instructions Harry Ungar referred to are in the FAQ at my site. They
tell how to add CONECT records to a PDB file which make RasMol/Chime show
double bonds.  There is also an example file there.

>    The second question is :
>    -What kind of glasses or goggles have to use to see in 3D the
>molecules in "3D mode" ?
>Can i find something about it on the Net? Or buy it somewhere?

I agree with Gale Rhodes that learning how to see the 3D, either cross-eyed
or wall-eyed, is the best solution.  However some people have much more
difficulty than others doing this, in which case the about $100 Nu3DVu
glasses may be worthwhile.  I have a pair which I never use except to show
people how cumbersome they are -- they do work but restrict your movements
and would be very fatiguing for prolonged use.

The professional solution, CrystalEyes, works without eyestrain, but costs
over $1,000 and in any case neither RasMol nor Chime supports the requisite
display mode (unlike e.g. the program O used widely by crystallographers).

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

References: <3678EEB7.BF138181@geocities.com>
++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: plug-in
Date: Thu, 17 Dec 1998 16:36:14 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

At 12/17/98, you wrote:
>Hi all,
>I am new to the area, I downloaded Chime and was asked for the plug-in
>chemical/x-xyz. However, cannot manage to download this plug-in.  Any
>suggestion?
>thanks in advance
>sonia
> 

This is not another plug-in but a MIME type which Chime should automatically
recognize. You'll have to give us a lot more detail to enable someone to
diagnose what your problem is. The most common reason I can't help people
is because they don't give me enough information to figure out what they're
doing. Also please identify yourself and where you are working.

-Eric Martz
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Albion Baucom <baucom@gorby.ucsc.edu>
Subject: Re: 3D glasses
Date: Thu, 17 Dec 1998 18:52:38 -0800 (PST)
To: rasmol@dhcp-srv2.oit.umass.edu

On Thu, 17 Dec 1998, Eric Martz wrote:

> The professional solution, CrystalEyes, works without eyestrain, but 
>costs over $1,000 and in any case neither RasMol nor Chime supports the
>requisite display mode (unlike e.g. the program O used widely by
>crystallographers).
> 
> -Eric

I can attest to the quality of the images created by these glasses. We use
them SGI workstations and they really do make the molecules jump out of
the screen. They do cause me some eye-strain though when I have used them
for extended periods (45 mins or more).

On the subject of mol viz programs we use UCSF MidasPlus 2.1 with our
Crystal Eyes. This is a very inexpensive ( less than $200
academic) program that works on workstations (SGI, DEC) and LINUX. It is
primarly command line based, but if you can script in RasMol or Chime you
can pickup the command syntax quickly. It makes really nice still images
that have lots of lighting and camera angle options as well.

The 3D image red-blue anaglyphs(?) does sound interesting if you could do
it IN RasMol or Chime. Maybe two models transformed by some amount in the
same MOL file and colored accordingly?

Albion

Albion Baucom
http://tito.ucsc.edu/baucom

X-MSMail-Priority: Normal
++++------+------+------+------+------+------+------+------+------+------+
From: "Van de Wiele Annie" <avandewiele@nordnet.fr>
Subject: to color non usual amino-acids 
Date: Mon, 21 Dec 1998 10:19:49 +0100
To: "rasmol lists" <rasmol@dhcp-srv2.oit.umass.edu>

To Rasmol users...

What are the colours to employ to display several non common amino-acids in
RasMol to respect the usual terms ?

Kind regards.

Annie

E.mail: avandewiele@nordnet.fr

 x-mac-creator="4D4F5353"
++++------+------+------+------+------+------+------+------+------+------+
From: Tim <tdriscol@unix.amherst.edu>
Subject: Mac Chime 2.0a install
Date: Mon, 21 Dec 1998 07:54:29 -0500
To: Rasmol List <rasmol@dhcp-srv2.oit.umass.edu>

Mac users,

I am having no success using Chime 2.0a on my Mac system.  I have
downloaded a number of copies from MDL's website and gone through the
installation procedure without any trouble;  however, when I try to load
a page from my local HD, I am given an error message that says Netscape
could not load Chime for the application/x-spt MIME type, either because
of insufficient memory or incorrect installation.  This error message
repeats for every button or structure that tries to load.  It's puzzling
because all of the correct Chime MIME types appear to be installed and
enabled (according to my about:plugins and Preferences menus).  I have
tried deleting the old pdb and spt MIME type definitions as per earlier
emails, but no luck.  Has this afflicted anyone else?

I am using a PowerComputing 200 (PowerMac equivalent) with Mac OS 8.1
and Netscape 4.5 (encrypted).  I have 56M RAM and usually allocate 20M
to Netscape, though I've given it as much as 30M without fixing this
problem.  I tried installing over Chime 1.0, and then I tried ripping
out Chime 1.0 and installing Chime 2.0a fresh.  Neither worked.

As an extra tidbit, my Chime 1.0 does not seem to be happy either
anymore.  I have been having problems loading structures even from local
disks.  I found only one fix for this Chime 1.0 problem, and this
doesn't work for the Chime 2.0a problem.   I had to open the Netscape
Edit/Preferences/Applications menu, select the pdb MIME type, then hit
okay WITHOUT MAKING ANY CHANGES.  Reloading the page subsequently
brought up the structure, and the rest of my seesion was error-free
(i.e., I didn't have to repeat this procedure for every page).  Has
anyone else had *this* problem?

BTW, all of the scripts, structures, and webpages that show these
problems have all worked without incident up until this quirk.

Help, anyone?

Merry Christmas,

Tim Driscoll

UMass Amherst
tdriscoll@amherst.edu

 x-mac-creator="4D4F5353"
++++------+------+------+------+------+------+------+------+------+------+
From: Timothy Driscoll <tdriscol@unix.amherst.edu>
Subject: [Fwd: Mac Chime 2.0a install]
Date: Mon, 21 Dec 1998 10:50:50 -0500
To: Rasmol List <rasmol@dhcp-srv2.oit.umass.edu>

A.R.C.Raine@bioc.cam.ac.uk wrote:

> Tim Driscoll wrote:
>
> > I am having no success using Chime 2.0a on my Mac system.  I have
> > downloaded a number of copies from MDL's website and gone through the
> > installation procedure without any trouble;  however, when I try to load
> > a page from my local HD, I am given an error message that says Netscape
> > could not load Chime for the application/x-spt MIME type, either because
> > of insufficient memory or incorrect installation.  This error message
> > repeats for every button or structure that tries to load.  It's puzzling
> > because all of the correct Chime MIME types appear to be installed and
> > enabled (according to my about:plugins and Preferences menus).  I have
> > tried deleting the old pdb and spt MIME type definitions as per earlier
> > emails, but no luck.  Has this afflicted anyone else?
>
> I have exactly the same problem, but I assumed that it was because I am
> using an out-of-date version of Navigator (3.01 Gold, on a PowerBook
> 5300cs).  I'm stuck too!
>
> Andrew
>
> --
> Dr. Andrew Raine, Department of Biochemistry, University of Cambridge,
> 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
> Tel: +44 1223 333744,  FAX: +44 1223 766002, email: A.R.C.Raine@bioc.cam.ac.uk
> WWW:http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/

--
********************
Timothy Driscoll
UMass Amherst
Molecular and Cellular Biology
Chemistry-Biology Interface Program
*
Department of Chemistry
Amherst College
Amherst, MA 01002
413 542 2738
*
http://merckx.chem.amherst.edu/tdriscoll/
********************

X-Authenticated: wm0p by cyrus.andrew.cmu.edu
X-Licensed-To: Site License
X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id LAA21813
++++------+------+------+------+------+------+------+------+------+------+
From: "Will McClure" <wm0p@andrew.cmu.edu>
Subject: Re: Mac Chime 2.0a install
Date: Mon, 21 Dec 1998 11:51:36 -0500
To: tdriscoll@amherst.edu, "Rasmol List" <rasmol@dhcp-srv2.oit.umass.edu>

Tim & Andrew,

  I had some problems with Nav 4.05 and the LiveConnect features of Chime
2.0a. These disappeared with Nav 4.07 (MacG3; OS8.0 or 8.1) and Chime 2.0a
runs fine. However, it is essential that the MIME type suffixes be changed
in Netscape for Chime 2.0a. The text from the "release notes" is copied
below.

-Will

*****
There are several new file extensions supported by Chime 2.0 on the
Macintosh. However, if
       you have installed a previous version of Chime you may not have these
file types defined
       within Netscape. To find out if these extension are defined, select
the About Plug-ins menu
       from Netscape¹s Help menu. You should see the following suffixes for
the MIME types defined
       in Netscape: 

        chemical/x-gaussian-cube    cub,cube  
        chemical/x-mdl-tgf          tgf,skc 
        chemical/x-csml             csm,csml 
        chemical/x-pdb              pdb,emb,embl 

       If these additional extensions are not defined you will not be able
to view files with
       these extensions in HTML files locally on your Macintosh. Since
Netscape doesn¹t
       automatically update the suffixes for predefined MIME types, you will
need to manually
       update Netscape¹s registry. To do this, following the procedure below
(this procedure
       is for Netscape versions 4.xx) 
       1. Select Preferences from the Edit menu. 
       2. Open the Navigator category folder and select Applications. 
       3. Select chemical/x-gaussian-cube and press the Delete button. 
       4. Select chemical/x-mdl-tgf and press the Delete button. 
       5. Select chemical/x-csm and press the Delete button. 
       6. Select chemical/x-pdb and press the Delete button. 
       7. Select the OK button to close the Preferences dialog. 
       8. Exit Netscape. 
       9. Restart Netscape, then select About Plug-ins from the Help menu.
You should now
       see the additional suffixes for the MIME types listed above.
*****

--On Mon, Dec 21, 1998 7:54 AM -0500 Tim <tdriscol@unix.amherst.edu> wrote: 

> Mac users,
> 
> I am having no success using Chime 2.0a on my Mac system.  I have
> downloaded a number of copies from MDL's website and gone through the
> installation procedure without any trouble;  however, when I try to load
> a page from my local HD, I am given an error message that says Netscape
> could not load Chime for the application/x-spt MIME type, either because
> of insufficient memory or incorrect installation. . . etc.

        Rasmol List <rasmol@dhcp-srv2.oit.umass.edu>
References: <641151.3123229896@mi646.bio.cmu.edu>
 x-mac-creator="4D4F5353"
++++------+------+------+------+------+------+------+------+------+------+
From: Timothy Driscoll <tdriscol@unix.amherst.edu>
Subject: Re: Mac Chime 2.0a install
Date: Mon, 21 Dec 1998 12:10:35 -0500
To: Will McClure <wm0p@andrew.cmu.edu>,

Wil,

Thanks for the speedy reply.  Unfortunately, my problem runs deeper.

I have updated the MIME types for Chime after each installation and found it
did not fix the problem.  I've also deleted and recreated the
"application/x-spt" MIME type, which is not listed as a problem in the Chime
installer readme but I seem to have trouble viewing.  This also did not help.

What is even more confounding is that Chime 2.0a works perfectly in our lab
(which has essentially the same machine, same system, and same Netscape 4.5),
except that I installed Chime on our lab computer when it first came out.  I'm
wondering if the installer could have a problem?

Tim Driscoll

Will McClure wrote:

> Tim & Andrew,
>
>   I had some problems with Nav 4.05 and the LiveConnect features of Chime
> 2.0a. These disappeared with Nav 4.07 (MacG3; OS8.0 or 8.1) and Chime 2.0a
> runs fine. However, it is essential that the MIME type suffixes be changed
> in Netscape for Chime 2.0a.

        Rasmol List <rasmol@dhcp-srv2.oit.umass.edu>
References: <641151.3123229896@mi646.bio.cmu.edu>
 <367E8104.424B9BAD@unix.amherst.edu>
++++------+------+------+------+------+------+------+------+------+------+
From: Andrew Good <gooda@bms.com>
Subject: Re: Mac Chime 2.0a install
Date: Mon, 21 Dec 1998 16:36:06 -0500
To: tdriscoll@amherst.edu
Cc: Will McClure <wm0p@andrew.cmu.edu>,

Timothy Driscoll wrote:

> Wil,
>
> Thanks for the speedy reply.  Unfortunately, my problem runs deeper.
>
> I have updated the MIME types for Chime after each installation and found it
> did not fix the problem.  I've also deleted and recreated the
> "application/x-spt" MIME type, which is not listed as a problem in the Chime
> installer readme but I seem to have trouble viewing.  This also did not help.
>
> What is even more confounding is that Chime 2.0a works perfectly in our lab
> (which has essentially the same machine, same system, and same Netscape 4.5),
> except that I installed Chime on our lab computer when it first came out.  I'm
> wondering if the installer could have a problem?
>
> Tim Driscoll
>
> Will McClure wrote:
>
> > Tim & Andrew,
> >
> >   I had some problems with Nav 4.05 and the LiveConnect features of Chime
> > 2.0a. These disappeared with Nav 4.07 (MacG3; OS8.0 or 8.1) and Chime 2.0a
> > runs fine. However, it is essential that the MIME type suffixes be changed
> > in Netscape for Chime 2.0a.

Tim,

  it is interesting you mention the installer. We have had the same problem
downlading the installer executable for NT and 98 on the PC recently, but when
I downloaded my first copy of Chime for an NT PC a month ago it worked without
any problems, symptomatic of what you have seen.
Andy Good

 x-mac-creator="4D4F5353"
++++------+------+------+------+------+------+------+------+------+------+
From: Timothy Driscoll <tdriscol@unix.amherst.edu>
Subject: Re. Mac Chime 2.0a install
Date: Tue, 22 Dec 1998 08:10:53 -0500
To: Rasmol List <rasmol@dhcp-srv2.oit.umass.edu>

This message has been posted at the Chime help site as well.  If you can
add anything to this, or it sounds very familiar, please let me know
because I have run out of good ideas (I still have lots of outrageous
ones).

 Thanks!

- Tim Driscoll

Chime support team:

Thank you for your prompt response to my message posted on the rasmol
list.  Unfortunately, I am still having trouble with the Mac Chime 2.0a.
Any help you can offer would be great.

I am unable to correctly install Chime 2.0a in the encrypted version of
NS Comm 4.5. I have tried all suggestions in your readme and on the
rasmol email list. When I try to load a page with Chime, I get an error
message that says NS could not access Chime 2.0a to view the MIME type
application/x-spt; please make sure the plugin is installed correctly
and enough memory is available. I have 25M allocated to NS. I have
reinstalled both NS and Chime multiple times.  I have removed all other
plugins besides Chime and the default. I have rebuilt my desktop. I do
notice two unusual things: in the NS Preferences menu, the Chime and
Quicktime icons are generic icons; also, when I delete the
application/x-spt MIME type and restart NS, it comes back dimmed in the
Preferences menu and I can not Edit or Delete it again. Two other people
have responded to the Rasmol list with similar symptoms, one on a Mac
laptop (Andrew Raine, 12/21/98) and one on a Windows system (Andrew
Good, 12/22/98).
When I remove 2.0a and reinstall 1.0, no structures will appear at
first. To get structures to come up I have to go into the NS Edit
Preferences menu, select the application/x-spt MIME type and choose
Edit, hit okay without changing anything, exit the Preferences menu, and
reload the page. I have noticed this problem on other Mac computers as
well, though not consistently.

I am copying this message to the rasmol list as well, in case someone
else can offer suggestions.

Thank you!

********************
Timothy Driscoll
UMass Amherst
Molecular and Cellular Biology
Chemistry-Biology Interface Program
*
Department of Chemistry
Amherst College
Amherst, MA 01002
413 542 2738
*
http://merckx.chem.amherst.edu/tdriscoll/
********************

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: group coloring bug with NMR pdb's and palette limitations
Date: Tue, 22 Dec 1998 09:20:38 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

I have found a 'color group' bug in RasMol 2.6-beta-2a (and Chime 2.0)
regarding multiple-model NMR files. Roger Sayle has confirmed it. The
purpose of this message is to document the bug, provide a workaround, and
discuss some related palette limitation issues which affect both RasMol and
Chime.

I wanted to color e.g. model 1 black, and all other models by group. I
found that if I try to
do this with 'select not model=1' the 'color group' command fails (entire
chain blue).

There is a related matter.  If you apply color group first, and then try to
use a single new color, you usually get 'unable to allocate shade'. I've
found that if you 'reserve' the additional color first, then apply group,
you can get both. The palette limitation which is responsible for this
behavior is explained below by Roger.

Back to the group coloring failure.

Here is an example (1cfc is a clean example file with no hetero atoms):

load nmrpdb 1cfc.pdb
set hetero off
wireframe off
backbone
background white
select model=1
color black
select not model=1
color group

The final 'color group' colors residues 1-148 blue.

select 1-148 and not model=1
same result, all blue, but for 1jsa.pdb (188 residues)
'color group' colors residues 1-188 blue and light blue.

select model>1
same result but with 1jsa,
'color group' colors residues 1-188 blue and red (nothing in between!).

Here is a script which when run following 'load nmrpdb 1cfc.pdb'
demonstrates the
problem

# this script illustrates the bug which prevents making one backbone black
# by excluding it from the models colored by group

restrict none
select all
color white

select hetero
color cpk
spacefill

select model=1 and not hetero
backbone 0
color black

select not (hetero or model=1)
backbone 0.4
color group

------------------

Here is a script which succeeds with a workaround (it was designed for 1jsa
hence the
hetero atom stuff). 1jsa is itself an anomalous pdb so is problematic for
testing (see below).

# Attempt to make one model black and others group (bug workaround).
# A black label doesn't prevent the 'unable to allocate shade' but
# a black dot surface does!

# show nothing
restrict none

# clear the palette
select all
color white

# make something we don't need black to reserve this color
select atomno=1
dots
color dots black

# color hetero cpk
select hetero
color cpk
spacefill

# color backbones group
select not hetero
backbone 0.4
color group # now the palette is consumed and no new colors can be assigned

# set one backbone to black
select model=1 and not hetero
backbone 0
color black # works because we reserved it earlier

# now that we've used the black, we can get rid of the dots
dots off

-------------
Roger Sayle's explanation of the palette limitations in RasMol (and Chime)
sent 12/21/98:

BEGIN QUOTE OF ROGER SAYLE

These limits are defined in "transfor.h". The two numbers that are 
defined are "ColourDepth" (the number of intensity levels per shade) 
and "LastShade" (the number of available shades). Multiply these 
two numbers together to give the number of spacefilling colours.
For completeness three extra colours are also required (for the 
background, the bounding box or axes, and the labels). Finally 
the apple macintosh must always reserve one extra colour, and the X 
Windows version requires five extra colours (for the menus etc).

Hence the number of colours available is: 

System   Colour Depth * Last Shade + Extra = Total 
8bit PC    16              15          3      243 
8bit Mac   16              14          4      228 
8bit UNIX  16              15          8      248 
Other PC?  32              31          3      995 
Other Mac  32              31          4      996 
Other UNIX 32              31          8     1000 

All eightbit platforms must use less than 256 colours (or else). 

The only thing that I'd recommend changing is to set last shade 
to 63 on sixteen, twentyfour or thirtytwo bit display depths. 
Colour depths have to be a power of two, and are probably already 
smooth enough on spheres and ribbons.

However this still doesn't solve the problem. As soon as you try 
group colours it will use all the available shades. For example, 
every residue of crambin will become a slightly different shade.

END QUOTE OF ROGER SAYLE

-------------
Notes on 1jsa.pdb:

The first atom is HETATM in group MYR. Both the leading HETATM MYR and the
subsequent atoms ATOM GLY are numbered residue 1.
This causes the following anomalies:
You cannot select gly and 1.
Clicking on the gly reports it as Group: MYR, while clicking on a bona-fide

myr atom reports it as           Hetero: MYR!

'structure' command fails (0 helices).
In order to fix this, HETATM MYR must be moved to the end of the protein
chain; giving it a nonconflicting group number seems advisable too. In
order to show the bond between the GLY 1 and the MYR, the TER record
between the C-terminal amino acid and the HETATM MYR must be removed.

-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: "Adrian Kornhauser (lab3)" <adrian@laguna.fmedic.unam.mx>
Subject: About creating animations.
Date: Wed, 23 Dec 1998 20:12:49 -0600 (CST)
To: RasMol List <rasmol@dhcp-srv2.oit.umass.edu>

Hi!

We just saw the nice animations made by WebLab ViewerPro. We would like to
know if there is an easy may to make animated gifs out of these
animations, other than saving multiple gifs one by one and then making an
animation. Or if someone has a quick way of doing them other than with
WebLab.

Adrian

++++------+------+------+------+------+------+------+------+------+------+
From: Seth Harris <sharris@uclink4.berkeley.edu>
Subject: movies to VCR
Date: Tue, 29 Dec 1998 20:27:02 -0800
To: rasmol list <rasmol@dhcp-srv2.oit.umass.edu>

>Dear All,
>I am a graduate student who has been working on a crystallography project.
>RasMol's scripting allows better presentation of the work options, I feel,
>and I am now trying to convert my movie scripts onto a VCR for presentation
>at a departmental seminar.
>	The graphics board I just got has a video out line, so the hardware
>should not be a problem.  Writing the RasMol movies works well, too.
>It's just one key step in getting the movie "captured" in a format that can
>be fed out to the VCR (like .avi ?)  Has anyone done this?  From perusing
>the archives of this list the best option seems to be to "set write true"
>and then run a script where instead of refreshing the view after each
>operation one writes out the image instead (e.g. "write pict prot1" then
>"rotate x 1" then "write pict prot2" and so on was the example used.)  I
>imagine this will work, as I could find a way to feed the series of still
>images into a movie editting program that came with the graphics card I
>got.  I was wondering, though, if there have been any advances in this
>regard...it just seems that RasMol is already streaming the images out
>nicely, so why break them apart again?  Is there a more direct route
>(other than videotaping the monitor!!)?
>Also, I was wondering if Chime might have a hand in this, but I am less
>familiar with its operations and suspect it might be limited by the
>comments I see in regard to not being able to write output (i.e. images) to
>the disk.
>	Finally, I realize that an alternate would be to use a computer
>projection screen (entail finding a compatible laptop to borrow).  I may
>well end up going with that approach, though it's harder then to send a
>copy home to the family!  Any suggestions from all those lecturing
>presenters on the list?  Thanks in advance,
>Seth
>p.s. Despite being right here at Berkeley I've only just recently started
>playing with the Berkeley version of RasMol --multiple pdb capabilities and
>all...I have seen warnings about its inability to run scripts that include a
>zap command on windows, and just now had a script run ok but then leave the
>program only semi-operational.  Before I walk up there and start knocking
>on doors, is there any documentation on the specifics of the extended
>features of UCB RasMol?  And are these incorporated into script-able
>commands, for instance the ability to change the selected molecule with
>some kind of "select" command extension rather than doing it with the menu
>in the
>"Molecules" window?
>Cheers and Happy New Year

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Seth Harris
Botchan Lab
UC Berkeley
(510)642-5932

++++------+------+------+------+------+------+------+------+------+------+
From: Jens Grabenstein <Jens.Grabenstein@surf24.de>
Subject: Re: movies to VCR
Date: Wed, 30 Dec 1998 12:31:16 +0100
To: <rasmol@dhcp-srv2.oit.umass.edu>

>Also, I was wondering if Chime might have a hand in this, but I am less
>familiar with its operations and suspect it might be limited by the
>comments I see in regard to not being able to write output (i.e. images) to
>the disk.
>	Finally, I realize that an alternate would be to use a computer
>projection screen (entail finding a compatible laptop to borrow).  I may
>well end up going with that approach, though it's harder then to send a
>copy home to the family!  Any suggestions from all those lecturing
>presenters on the list?  Thanks in advance,
>Seth

I am working on a prototype of a tutorial using Chime in order to present 
it in lectures. So far we had very good results in using a PROXIMA 9600 
video beamer and a Compaq PII-266Mhz Laptop. It looks great! I used 
Eric's chime sample pages as template and inserted my scripts into it. 
You can take a look on it at 
<http://strucbio.biologie.uni-konstanz.de/~jensG/chime_tutorial/index.html>
.
You can also download the complete tutorial if you want to have a closer 
look on the source (http://strucbio.biologie.uni-konstanz.de/~jensG)

Jens

The optimist believes we live in the best of all worlds;
the pessimist fears this is so.
-----------------------------------------------------------
Visit my website: http://home.surf24.de/~grabenst/
-----------------------------------------------------------
E-mail: Jens.Grabenstein@surf24.de
        Jens.Grabenstein@uni-konstanz.de
-----------------------------------------------------------
Made with an Apple Macintosh, the only computer brand

++++------+------+------+------+------+------+------+------+------+------+
From: Eric Martz <emartz@microbio.umass.edu>
Subject: Re: movies to VCR
Date: Wed, 30 Dec 1998 12:20:09 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

In response to Seth Harris,

1. I strongly recommend making Chime presentations rather than RasMol
"movies". RasMol's strength lies in self-directed exploration of a molecule
by one person. Chime's strength is in presentations. Complete instructions
are at

Presenting RasMol-Saved Scripts with Chime

http://www.umass.edu/microbio/chime/prsswc/template.htm

...where you can download a template and instructions.  You can make a
state-of-the-art presentation without knowing any javascript (it is built
into the template already) and knowing only a few very simple elements of
HTML.  You do have to know how to use RasMol (see RasMol Quick Start,
http://www.umass.edu/microbio/rasmol/rasquick.htm)

2. I strongly recommend projecting presentations directly from Chime (or
RasMol) with a computer projector.  These projectors are becoming very
common at US institutions and if your Dept can't loan you one, most likely
your audio-visual dept. can.  IMHO this has huge advantages over making a
video movie tape, not the least being the ease of making revisions at the
last minute.

3. For information about UCB-RasMol, contact Marco Molinaro
(molinaro@lcbvax.cchem.berkeley.edu). As far as I know there has been no
debugging nor development of UCB-RasMol for several years. See
http://www.umass.edu/microbio/rasmol/getras.htm#top

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor (Immunology), Dept Microbiology
Morrill IVN 203, U Mass, Amherst MA US 01003-5720
413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu

Molecular visualization in bioscience education at the
RasMol Home Page <http://www.umass.edu/microbio/rasmol>
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

++++------+------+------+------+------+------+------+------+------+------+
From: Seth Harris <sharris@uclink4.berkeley.edu>
Subject: chime install
Date: Wed, 30 Dec 1998 16:23:56 -0800
To: rasmol list <rasmol@dhcp-srv2.oit.umass.edu>

Thanks for the tips in regard to chime movies vs. VCR.  Sounds like I
should go with chime.  I started in on it and its been a mix of excitement
and frustration.  To wit, download was ok and installation appears fine,
only the most important (in my view) file format is not enabled...the x-pdb
format so I always get the broken plug-in icon for all the images I'd
really like to look at.  Some of the MDL samples of small molecules work
fine.  So...I tried to find a mime.config file or some other suitable place
to add the lines to support all file types (using Navigator 4.0.4 and Chime
2.0a) but without success.  Currently on a Mac but have a PC at home...any
tips on how to get the pdb's working and where to then learn HTML?  I've
got about a week to get all this together!!  Thanks,Seth
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Seth Harris
Botchan Lab
UC Berkeley
(510)642-5932

References: <v04011700b2b073b79213@[128.32.128.22]>
 x-mac-creator="4D4F5353"
++++------+------+------+------+------+------+------+------+------+------+
From: Timothy Driscoll <tdriscol@unix.amherst.edu>
Subject: Re: chime install
Date: Thu, 31 Dec 1998 08:10:25 -0500
To: rasmol@dhcp-srv2.oit.umass.edu

Seth Harris wrote:

> Thanks for the tips in regard to chime movies vs. VCR.  Sounds like I
> should go with chime.  I started in on it and its been a mix of excitement
> and frustration.  To wit, download was ok and installation appears fine,
> only the most important (in my view) file format is not enabled...the x-pdb
> format so I always get the broken plug-in icon for all the images I'd
> really like to look at.  Some of the MDL samples of small molecules work
> fine.  So...I tried to find a mime.config file or some other suitable place
> to add the lines to support all file types (using Navigator 4.0.4 and Chime
> 2.0a) but without success.  Currently on a Mac but have a PC at home...any
> tips on how to get the pdb's working and where to then learn HTML?  I've
> got about a week to get all this together!!  Thanks,Seth
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Seth Harris
> Botchan Lab
> UC Berkeley
> (510)642-5932

Seth,

I've also had problems with Chime 2.0a on the Mac and MIME types.  According to MDL
(search the rasmol email list past history for the exact messages), try deleting
the pdb MIME type under Netscape Edit/Preferences/Applications, then quit and
restart Netscape.

As for html, I recommend The BareBones Guide to HTML found at

    http://werbach.com/barebones/barebone.html

as a starting point.  You can also find the basic HTML necessary to modify Eric
Martz's Chime tutorials in the tutorial packages themselves - just open up the html
documents in a text editor like BBEdit or MS Word and read the comments.

Good Luck!

Tim Driscoll

********************
Timothy Driscoll
UMass Amherst
Molecular and Cellular Biology
Chemistry-Biology Interface Program
*
Department of Chemistry
Amherst College
Amherst, MA 01002
413 542 2738
*
http://merckx.chem.amherst.edu/tdriscoll/
********************

++++------+------+------+------+------+------+------+------+------+------+
END OF 98.11-12