Beginning Jan 1, 1999: ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton" Subject: Video taping computer presentation Date: Mon, 04 Jan 1999 10:17:05 -0800 To: rasmol list Cc: SethHarris Seth Harris wrote: >...I am now trying to convert my movie scripts onto a VCR > for presentation at a departmental seminar. If you can hook your computer video out to a TV (i.e., show what is on the computer on a TV screen "live"), you should be able to hook it to a VCR just as easily. You should be able to use the computer like any other video source. Be aware that TV resolution is not nearly as good as computer monitor resolution, so it may be difficult for your audience to see small details (like labels or other text). Be sure to adjust text sizes and so forth to be large enough. I find that settings that are easy to see on a 640x480 screen usually translate marginally well to a TV, but most screens that are used at higher resolutions try to fit too much on the screen to work on a TV. A computer projector would have much better resolution (most of the middle-of-the-road projectors use true 800x600 resolution.) -- Robert M. Horton, Ph.D. 0 []~ ~ ~ ~ http://www.attotron.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton" Subject: Chime presentation Date: Mon, 04 Jan 1999 10:37:07 -0800 To: rasmol list Cc: Seth Harris Seth; I am working on a Javascript-based Chime Scripting Wizard to help folks make presentations with Chime. The bad news is the project isn't very far along. The good (?) news is, I'm looking for presentations to make myself to try my metascripts. Make ya a deal: I'll (try to) help with your presentation if you agree to give me feedback on my Scripting Wizard if and when I get parts of it done. If you're really desperate, I can even loan you a laptop and projector (if you can come get them in Sacramento...) -- Robert M. Horton, Ph.D. 0 []~ ~ ~ ~ http://www.attotron.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- References: <004501be1a8c$9c23fb60$f370fed0@yeeho> <365FC723.F8BA7509@inn-prot.weizmann.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: vdW radii Date: Tue, 05 Jan 1999 15:31:20 +0100 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------B7225FA63FE74686BB1BC40D --------------A8D9598D2303587319BBA012 > Hi, Dear Rasmolians: We are preparing some websites with supramolecular structures represented by chime (still under construction): http://www.uni-sb.de/matfak/fb11/schneider/supram/supramolecular_structures.html I looked up some old emails from the RasmolList about atomic radii, but I still got a problem with the vdW radii in chime/rasmol: What is the default value for the spacefilling command (500 seems to be too high, 400 too small) if I use the pull down option in Rasmol (spacefilling --> vdW)? Is there any (easy) way to define vdW radii? As far as I know there is no information in a pdb file about atomic charges. Is this the reason why our 18C6/potassium complex looks that strange in the spacefilling model? (vdW radii for K and K+ are the same?!!) (see attached file) --------------A8D9598D2303587319BBA012
 Hi, Dear Rasmolians:


We are preparing some websites with supramolecular structures represented by chime (still under construction):

http://www.uni-sb.de/matfak/fb11/schneider/supram/supramolecular_structures.html

I looked up some old emails from the RasmolList about atomic radii, but I still got a problem with the vdW radii in chime/rasmol:
What is the default value for the spacefilling command (500 seems to be too high, 400 too small) if I use the pull down option in Rasmol (spacefilling --> vdW)?

Is there any (easy) way to define vdW radii?

As far as I know  there is no information in a pdb file about atomic charges.
Is this the reason why our 18C6/potassium complex looks that strange in the  spacefilling model? (vdW radii for K and K+ are the same?!!) (see attached file)
  --------------A8D9598D2303587319BBA012-- --------------B7225FA63FE74686BB1BC40D Content-Disposition: inline; filename="18C.PDB" HETATM 1 O 1 2.948 0.000 0.244 1.00 0.00 HETATM 2 C 2 3.488 1.188 -0.304 1.00 0.00 HETATM 3 C 3 2.776 2.424 0.284 1.00 0.00 HETATM 4 O 4 1.472 2.552 -0.260 1.00 0.00 HETATM 5 C 5 0.712 3.616 0.284 1.00 0.00 HETATM 6 C 6 -0.712 3.616 -0.300 1.00 0.00 HETATM 7 O 7 -1.472 2.552 0.248 1.00 0.00 HETATM 8 C 8 3.488 -1.192 -0.300 1.00 0.00 HETATM 9 C 9 2.776 -2.428 0.292 1.00 0.00 HETATM 10 O 10 1.472 -2.556 -0.248 1.00 0.00 HETATM 11 C 11 0.712 -3.620 0.300 1.00 0.00 HETATM 12 C 12 -0.712 -3.620 -0.288 1.00 0.00 HETATM 13 O 13 -1.472 -2.552 0.256 1.00 0.00 HETATM 14 C 14 -2.776 2.424 -0.296 1.00 0.00 HETATM 15 C 15 -3.488 1.188 0.296 1.00 0.00 HETATM 16 O 16 -2.948 0.000 -0.248 1.00 0.00 HETATM 17 C 17 -2.776 -2.428 -0.284 1.00 0.00 HETATM 18 C 18 -3.488 -1.192 0.300 1.00 0.00 HETATM 19 K 19 0.000 0.000 0.000 1.00 0.00 TER 20 19 END --------------B7225FA63FE74686BB1BC40D Content-Description: Card for Frank Eblinger Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Frank Eblinger n: Eblinger;Frank adr: In den Welkertswiesen 65;;;Saarbrücken;Saarland;66125;Germany email;internet: f.eblinger@rz.uni-sb.de title: Dr. tel;work: 0681-302-3949 tel;fax: 0681-302-4105 tel;home: 06897-764132 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------B7225FA63FE74686BB1BC40D-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Hens Borkent Subject: Chime XYZ animations, mol editor Date: Fri, 08 Jan 1999 11:34:21 +0100 To: rasmol@dhcp-srv2.oit.umass.edu, mitch@mdli.com Chimers of the world, There have been several questions lately about Chime animations, based on multiple XYZ files. We have been using these animations for quite a while now, in our educational (organic chemistry) web pages Molecules in four dimensions (http://www.caos.kun.nl/wetche/organic/), Mol4D. Besides ready-made animations, Mol4D features a perl script based Chime molecule editor, to edit mopac input files and produce Chime'd xyz animations on the fly. (Netscape/Windows/MacPPC preferred) We have decided to make all the scripts available to the chime-using community. At the bottom of the page mentioned above there is a link to the 'technical background', that explains which script is used for what. The scripts are to some extent site-specific, of course, but could be adapted for local use. We would like to encourage the use of these scripts, in both ways: improvements on their tasks, and developing more applications in the field of organic chemistry. We intend to maintain a repository of the results, so please inform us if you have a contribution that is useful for others. -- ***** J.H. (Hens) Borkent, CAOS/CAMM Center, *CAOS * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CAMM* e-mail: borkent@caos.kun.nl ***** http://www.caos.kun.nl/staff/borkent.html pdb-l@pdb.pdb.bnl.gov bourne@sdsc.edu, helgew@sdsc.edu, jls@bnl.gov ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer/Comparator version 0.95 w/ NMR support Date: Sun, 10 Jan 1999 21:52:40 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu, Cc: rhodes@usm.maine.edu, brian.white@umb.edu, cmartin@chem.umass.edu, I put a new version of my Protein Explorer/Comparator at http://www.umass.edu/microbio/chime/explorer This version has all functionality that I have planned for version 1.0, designed to provide a RasMol-like interface in Chime. It is designated version 0.95 only because I have not yet written the tutorial for beginners, but those experienced with RasMol will have no problem using it. It is not yet linked to my public site pending completion of the tutorial; hence, this email announcement is its only publicity at this time. I would value feedback from anyone interested, especially Macintosh users. The entire package can be downloaded for local use. This version requires Chime 2.0, hence will work only on Windows95/NT4 or Macintosh PPC, and it requires Netscape Navigator 4.04 or later (4.5 recommended); Internet Explorer won't work properly. For SGI users, I have left the previous version 0.92 (which supports Chime 1.0 and, tho untested by me, may work with SGI Chime 0.9e) -- you'll see the link from the above URL. The Protein Explorer includes a command line input slot and a box for messages from Chime or from the Explorer itself. It allows you to load any PDB file from your disk, or via Internet from the closest mirror of the PDB. Convenience buttons are provided for spin, zoom, background color, water, hetero atoms. I have put a lot of effort into convenience features for exploring multiple-model NMR PDB files. When NMR files are loaded, the number of models is automatically detected, and an NMR control panel is offered. Initially, all models are shown overlayed. There are buttons to show one model at a time (in order, or any model you specify). There is a slot in which you can specify a list of particular model numbers, in any order. There is an [Auto] button which automatically steps through all models, one at a time, or the list of models you have specified in the order specified. You can specify one model as a reference model, and it is represented (by default) in black -- this model is always shown as you cycle through the other models. While Auto-stepping through a list of models, you can interrupt at any model and the Explorer will report which model you have selected. You can specify a custom color-scheme or rendering script which will supercede the defaults for all of the above features. All of these features also work in the Comparator, where you have two Chimes, so you can load two different PDB files (or the same file twice) and make side by side comparisons. The Comparator now includes a [Synch] button which makes one molecule follow all mouse-directed movements of the other molecule. This feature was added to Chime 2.0 by Tim Maffett, at my suggestion, just before it was released. I have included a document "Purpose of the Protein Explorer" which briefly discusses the history of Chime use, starting with linear tutorials on author-selected molecules (a la kinemages), and progressing to focussed tools which operate on a user-selected molecule (e.g. STING, Noncovalent Bond Finder, viewer for PDB Lite), and now to the Explorer, a totally general interface which invites the user to load any molecule and do anything of which Chime is capable. The long-range goal of the Protein Explorer (for future versions) is to make exploration and understanding of 3D structure more accessible to the general scientific public (educators, nonspecialists, and occasional users). I hope crystallographers and structure researchers will also find useful some of the convenience features which go beyond RasMol. It is planned to incorporate the Explorer directly into the PDB search interface. Cookies are used, and to reassure those who are worried about cookies, we have provided what I hope you'll agree is a thorough and authoritative discussion. The conclusion is not to worry; but you're told how to worry effectively if you insist. The Explorer/Comparator is free to all users (thanks to the NSF's Division of Undergraduate Education and UMass for support). Although it can be used directly from the web, it can also be downloaded for the convenience of local use. TECHNICAL INFORMATION This version first includes javascript for unscrambling the messages received from Chime via MessageCallback. This turned out to be complex but seems to be working reliably. The code for unscrambling alone exceeds 400 lines. The version/design document which is provided with the Explorer explains in more detail how this interface works. The scrambling which occurs is not due to a bug in Chime, according to Tim Maffett, but occurs somewhere in the 'black box' of the LiveConnect interface with Netscape. Hence it is not under the control of MDLI. Unscrambling is necessary to allow javascript to query Chime unambiguously for critical information such as how many NMR models were loaded, which model is displayed after interrupting auto-stepping, how many atoms are selected by a given command, etc. It is also necessary so that javascript can tell when Chime has completed executing a script, which in turn can be used not only to signal the user with a Ready/Busy indicator, but also to prevent sending a new script to Chime immediately following an interrupt, which results in interscrambling of both scripts (a condition even my 400+ line unscramble() can't deal with). Other developers of Chime resources may wish to use the unscrambling mechanism in their own work and are welcome to do so. Just download the Explorer and you get this code plus detailed documentation with it. Start in the Design Features document which directs you to the relevant functions and files. Happy 1999 to all rasmolians/chimeleons, -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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Mark Brooks Subject: Compiling Rasmol under Linux Date: Mon, 11 Jan 1999 20:20:54 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Hi! Sorry for asking another linux question, but I'm having a bit of a problem compiling Rasmol in Red Hat linux 5.2. I'm using the RasMol26 file from "ftp://nexus.roko.goe.net/pub/rasmol/" as told in the discussion group's history, and have defined "#define USE_FD_SET_TYPE" and 16bit for my display as instructed (I hope), but I still get the following output when I make it: [root@reeves RasMol2.6x1]# make gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -I/include -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DSIXTEENBIT -c rasmol.c -o rasmol.o rasmol.c: In function `ResetTerminal': rasmol.c:220: `TCSETAW' undeclared (first use this function) rasmol.c:220: (Each undeclared identifier is reported only once rasmol.c:220: for each function it appears in.) rasmol.c: In function `InitTerminal': rasmol.c:517: `TCGETA' undeclared (first use this function) rasmol.c:518: `IntrTerm' has an incomplete type rasmol.c:520: invalid use of undefined type `struct termio' rasmol.c:521: invalid use of undefined type `struct termio' rasmol.c:522: invalid use of undefined type `struct termio' rasmol.c:523: invalid use of undefined type `struct termio' rasmol.c:525: invalid use of undefined type `struct termio' rasmol.c:526: invalid use of undefined type `struct termio' rasmol.c:529: invalid use of undefined type `struct termio' rasmol.c:532: `TCSETAW' undeclared (first use this function) rasmol.c: At top level: rasmol.c:117: storage size of `OrigTerm' isn't known rasmol.c:118: storage size of `IntrTerm' isn't known make: *** [rasmol.o] Error 1 What could I be doing wrong please? Any advice to get this wonderful software working would be greatly appreciated! Thanks in advance, Mark. Mark Brooks, Institute of Neuropathology, CWRU, Cleveland, OH., 44106. Tel: (216) 368 3329. ++++------+------+------+------+------+------+------+------+------+------+ From: Albion Baucom Subject: Re: Compiling Rasmol under Linux Date: Mon, 11 Jan 1999 17:42:07 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu You may have a problem with includes and their paths. Under Linux 5.2 termio.h is in /usr/include, but it should be in the directory /usr/include/sys. To try this fix make a COPY of termio.h in /usr/include/sys and try a clean make (make clean, make). If this works let me know since people in our lab have had problems with this as well and havent got passed it yet. GCC is complaining that the functions ResetTerminal and InitTerminal cannot find the delerations for TCSETAW and TCGETA and the C struct termio which are all declared in termio.h since it can't find the file termio.h in /usr/include/sys. The Makefile is where the information about where includes are kept so if you are brave you can use a text editor to pick through this to find where the Makefile is looking for the termio.h and change it to the correct location (or make a copy as suggested above which is an easier patch at this point). Good luck! Albion Albion E. Baucom '71 R75/5 '74 R75/5 http://tito.ucsc.edu/baucom On Mon, 11 Jan 1999, Mark Brooks wrote: > Hi! > Sorry for asking another linux question, but I'm having a bit of a > problem compiling Rasmol in Red Hat linux 5.2. > > I'm using the RasMol26 file from > "ftp://nexus.roko.goe.net/pub/rasmol/" > as told in the discussion group's history, and have defined "#define > USE_FD_SET_TYPE" and 16bit for my display as instructed (I hope), but I > still get the following output when I make it: > > [root@reeves RasMol2.6x1]# make > gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -I/include > -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE > -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 > -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DSIXTEENBIT -c > rasmol.c -o rasmol.o > rasmol.c: In function `ResetTerminal': > rasmol.c:220: `TCSETAW' undeclared (first use this function) > rasmol.c:220: (Each undeclared identifier is reported only once > rasmol.c:220: for each function it appears in.) > rasmol.c: In function `InitTerminal': > rasmol.c:517: `TCGETA' undeclared (first use this function) > rasmol.c:518: `IntrTerm' has an incomplete type > rasmol.c:520: invalid use of undefined type `struct termio' > rasmol.c:521: invalid use of undefined type `struct termio' > rasmol.c:522: invalid use of undefined type `struct termio' > rasmol.c:523: invalid use of undefined type `struct termio' > rasmol.c:525: invalid use of undefined type `struct termio' > rasmol.c:526: invalid use of undefined type `struct termio' > rasmol.c:529: invalid use of undefined type `struct termio' > rasmol.c:532: `TCSETAW' undeclared (first use this function) > rasmol.c: At top level: > rasmol.c:117: storage size of `OrigTerm' isn't known > rasmol.c:118: storage size of `IntrTerm' isn't known > make: *** [rasmol.o] Error 1 > > What could I be doing wrong please? Any advice to get this wonderful > software working would be greatly appreciated! Thanks in advance, > > Mark. > > Mark Brooks, > Institute of Neuropathology, > CWRU, Cleveland, OH., 44106. > Tel: (216) 368 3329. > ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Compile Rasmol Date: Wed, 13 Jan 1999 22:36:41 -0800 (PST) To: Rasmol Help I am using visual c++5.0 to compile rasmolv2.5 on a windows95 os.I am getting the following error: Raswin.obj:error LNK2001: unresolved external symbol _fstrnicmp .Could anyone help me in this problem or can anyone help in the compilation of rasmol. Thanks a lot in advance. Bye& _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com References: <19990114063641.21175.rocketmail@send105.yahoomail.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Compile Rasmol Date: Thu, 14 Jan 1999 13:56:40 +0000 To: rasmol@dhcp-srv2.oit.umass.edu James Leong Mook seng wrote: > > I am using visual c++5.0 to compile rasmolv2.5 on a windows95 os.I am > getting the following error: Raswin.obj:error LNK2001: unresolved > external symbol _fstrnicmp .Could anyone help me in this problem or > can anyone help in the compilation of rasmol. Thanks a lot in advance. > Bye& Hi, I've used MS-C++ v.5.0 to compile Rasmol2.6b - but that's a long time ago ;-). The only 'help' I can give at the moment is to define '_WIN32' manually in rasmol.h. You do this by putting the line #define _WIN32 somewhere at the beginning of rasmol.h. The compiler (pre-compiler) then uses strnicmp instead of _fstrnicmp! I guess the whole '_f' stuff is something comming from win3.1 ... . Don't know if that works, let me know about the result (I'm sory I cannot test it as I've no win95 machine here), good luck, 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-pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael Meredith" Subject: How do you show sections of molecules? Date: Thu, 14 Jan 1999 15:09:10 -0000 To: rasmol@dhcp-srv2.oit.umass.edu Can you help? I'm trying to compile a tutorial in RasMol and want to display only sections of some chains. I know how to restrict views of molecules to chains, but I only want to show part of a chain at a time. Thanks for you help, Michael ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Ideas solicited for Protein Explorer 0.96 Date: Thu, 14 Jan 1999 12:50:06 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I've had some feedback from Macintosh users about the Protein Explorer 0.95, and a couple of new ideas myself. Here are my plans for version 0.96. Comments and suggestions to add to this list are welcome (tho I can't promise to do them all). New features planned: * User-configurable aliases. These are just typing conveniences. For example 's l' will expand to 'select ligand', 's 122-160 and n w' will expand to 'select 122-160 and not water' (can't alias 'a' to 'and' since 'a' already means adenosine), 'cs' will expand to 'center selected', 'spm' will expand to 'set picking monitor', etc. If you want to suggest other default aliases, the complete list I have in mind is below. Would anyone want 1-letter AA codes aliased? I don't plan to do it unless interest is expressed as it involves a bit of extra coding. It would be a user-enabled preference, not a default. Since a, t, g, c conflict with nucleotides, if you enabled this and then wanted to refer to nucleotides, you'd have to prefix them with a period, which will prevent alias expansion (for example 's .a,.t' would expand to 'select a,t' instead of 'select ala,thr'.) * User-configurable project folder(s). By default, RasMol's load command looks for PDB files in the folder from which it was started (or the working folder specified in a Windows shortcut icon). Similarly, the 'script' command looks for .spt files in that folder. PE does the same but its working folder is 'explorer' which already contains over 50 files not relevant to a particular project. I'll add the capability to set a project folder (for PDB files and scripts), and optionally different folders for scripts (primary and secondary). The secondary script folder would be for scripts shared between projects. What this means is that the commands 'load xxx.pdb' or 'script xxx.spt' will automatically get the specified project path prefixed to xxx. Unfortunately I have no way to change the present default that saving a PDB file from Chime puts the file in Netscape's program folder. * Thanks to the suggestion of Kurt Giles, I'll add an 'edit preferences' capability. His suggestion was to be able to start with spin off. Other ideas: automatically add .pdb to the filename in a load command, and .spt to the filename in a script command. And it might be useful to be able to turn off alias expansion. Any other ideas for preferences? (The preferences will be saved as a cookie so will survive between sessions.) Macintosh fixes: * After pressing Enter to send a manually typed command, the focus will be forced back to the command slot so you don't have to click there before typing the next command. (This is already the case under Windows). * 'Force ready' (you have to scroll below the message area to see it) will be improved to work reliably with a single click. This allows you to recover from the permanent busy condition which presently results from resizing the PE or Chime windows. Several people have reported that the [Synch] button doesn't work on Macintoshes. That's a bug which slipped by into Chime 2.0a and is not under my control (it has been reported to MDLI). I'll add a message which informs Mac users not to expect it to work. Here is the complete list of aliases which will ship with the PE (you can change these or add new ones but these will be the default): cs center selected js javascript l ligand ll lload ls lscript m (cadmium,calcium,iron,magnesium,manganese,zinc) n not s select sc script w water spi set picking identify spd set picking distance spm set picking monitor spa set picking angle spt set picking torsion spl set picking label spc set picking center nn funny funny not(protein,dna,rna,hetero) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ rasmol@dhcp-srv2.oit.umass.edu References: <369DF798.E5783CBA@icrf.icnet.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: How do you show sections of molecules? Date: Thu, 14 Jan 1999 13:15:28 -0500 To: michael.meredith@continuing-education.oxford.ac.uk, For section of residues 23-44 in chain :a, 'restrict 23-44:a'. Or 'restrict none', then 'select 23-44:a', then render and color as desired. All this and more is explained in Select Commands in Chime and RasMol http://www.umass.edu/microbio/rasmol/seleccmd.htm At 1/14/99, Michael Meredith wrote: >Can you help? > >I'm trying to compile a tutorial in RasMol and want to display only >sections of some chains. I know how to restrict views of molecules >to chains, but I only want to show part of a chain at a time. > >Thanks for you help, > >Michael > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Color Date: Fri, 15 Jan 1999 21:32:14 -0800 (PST) To: Rasmol Help How can i customise the color of atoms(H,C, etc) in rasmolv2.5.Thank you very much in advance.& _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Recent stats for RasMol/Chime site Date: Sun, 17 Jan 1999 13:43:25 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Below are numbers of 'people' visiting my molecular visualization freeware site, where it is interesting to see the holiday/new-year dip. There is also an analysis of the past week's activity at the Chime branch. As I have seen in the past, the majority (70-90%) of people who visit my Chime resources never go very deep into them, which I interpret to mean that they don't have Chime installed. It is unfortunate that so many miss out due to the 'energy barrier' of the downloading and installation. A result which surprised me is that there appears to be more interest in the Noncovalent Bond Finder than in any other single topic/resource I have authored and provided on my Chime site. Here are the recent numbers of distinct IP addresses coming to my UMass Chime site, the RasMol Home Page, and the total. The total is less than the sum since many visitors go to both. The number of files fetched is on the order of 20 times these numbers. > Unique IP Addresses > -------------------- >Week ending Chime RasMol Total >Feb /97 831 2,746 2,929 (Dates are Month/Day/Year following US convention) >11/15/97 1,205 2,943 3,243 >02/07/98 1,448 3,502 3,897 >11/07/98 2,545 5,632 6,263 >11/28/98 2,133 4,578 5,163 (thanksgiving) >12/05/98 2,285 5,092 5,719 >12/12/98 2,068 4,521 5,128 (Christmas shopping?) >12/19/98 1,812 4,425 4,942 ditto >12/26/98 948 2,113 2,376 Xmas! > >01/02/99 898 1,917 2,195 New Years! >01/09/99 1,816 3,835 4,351 >01/16/99 2,163 4,499 5,192 The following details are for the week of January 10-16 1999 for the Chime site only. The number of distinct IP addresses ("people") visiting the site was 2,163 (as shown above). Numbers below (unless otherwise indicated) are numbers of times the indicated file was fetched. One visitor can fetch the same file more than once. In the Overview, MainPage is the number of fetches of index.htm (or equivalent), while Deeper is the number of fetches of a page not likely to be fetched unless Chime is installed. OVERVIEW (week of 1/10-16/99) Branch MainPage Deeper NCB Finder 472 65 (247 people; 21 people did 664 finding cycles!) DNA 342 95 Chime: How 271 30 Explorer 240 48 Hemoglobin 106 25 Template 100 20 (template for creating Chime presentations) ProtSecS 76 37 (non-supported, obsolete version) Antibody 73 8 MHC 50 4 Morpher 48 17 Downloads 263 n.a. (fetches of above chime packages for local use) World Index 371 n.a. (just a document) The astonishing thing here is the level of interest in the Noncovalent Bond Finder! Also amazing is the interest in the Explorer considering that is is not linked to my site (still a beta-test version), and has been announced only to about 1,000 people (PDB list and RasMol list). This may be a novelty effect for the Explorer, but the Finder has been on the web since April '98 and nothing has been done to it since (except for a minor fix to accomodate Chime 2 for Macs after its release in early Nov '98). The Finder is not available for download pending ongoing discussions about how best to support its future development. The Explorer is free to all users and was downloaded 42 times during the week. If anyone is interested, send me a request by email and I can provide a more detailed set of numbers for each of the above 'branches' (or even the raw web logs). /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <0F5P00453VUPZZ@rfd1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Chen Hsiung Chan Subject: Re: Recent stats for RasMol/Chime site Date: Mon, 18 Jan 1999 02:55:48 +0800 To: rasmol@dhcp-srv2.oit.umass.edu On Sun, Jan 17, 1999 at 01:43:25PM -0500, Eric Martz wrote: [snipped] > There is also an analysis of the past week's activity at the Chime branch. > As I have seen in the past, the majority (70-90%) of people who visit my > Chime resources never go very deep into them, which I interpret to mean > that they don't have Chime installed. It is unfortunate that so many miss > out due to the 'energy barrier' of the downloading and installation. [snipped] There is indeed a energy barrier, but not from 'downloading and installation'. I am a FreeBSD/Linux/Digital Unix(alpha) user. Unfortunatelly chime does support these platforms. -- 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: <0F5P00453VUPZZ@rfd1.oit.umass.edu> <19990118025548.B5424@waru.life.nthu.edu.tw> ++++------+------+------+------+------+------+------+------+------+------+ From: Chen Hsiung Chan Subject: Re: Recent stats for RasMol/Chime site Date: Mon, 18 Jan 1999 03:30:44 +0800 To: rasmol@dhcp-srv2.oit.umass.edu On Mon, Jan 18, 1999 at 02:55:48AM +0800, Chen Hsiung Chan wrote: > On Sun, Jan 17, 1999 at 01:43:25PM -0500, Eric Martz wrote: > [snipped] > > There is also an analysis of the past week's activity at the Chime branch. > > As I have seen in the past, the majority (70-90%) of people who visit my > > Chime resources never go very deep into them, which I interpret to mean > > that they don't have Chime installed. It is unfortunate that so many miss > > out due to the 'energy barrier' of the downloading and installation. > [snipped] > > There is indeed a energy barrier, but not from 'downloading and > installation'. I am a FreeBSD/Linux/Digital Unix(alpha) user. > Unfortunatelly chime does support these platforms. Oops. I lost the 'not'. Clearly I should not reply/post anything at 3:00am. -- 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: <19990116053214.9490.rocketmail@send1e.yahoomail.com> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Color Date: Mon, 18 Jan 1999 08:12:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu James Leong Mook seng wrote: > How can i customise the color of atoms(H,C, etc) in rasmolv2.5.Thank > you very much in advance.& > > _________________________________________________________ > DO YOU YAHOO!? > Get your free @yahoo.com address at http://mail.yahoo.com James, One way to do this is to write a script using any generic text editor (WordPad, BBEdit), save it, then call it in Rasmol whenever you want to apply the color scheme. Your script (mycolors.spt) might look something like this, for example: # script mycolors.spt select carbon color [255,0,0] #red carbons select oxygen color [255,255,255] #white oxygens select nitrogen color [0,0,255] #blue nitrogens select hydrogen color [160,32,240] #purple hydrogens etc... and you can call it by typing 'script mycolors.spt' in the Rasmol command line. N.B. Be careful to put the script file in the same folder/directory as the Rasmol program or the script won't run. Happy coloring! 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/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Load a file automatically. Date: Mon, 18 Jan 1999 07:18:13 -0800 (PST) To: Rasmol Help Hello, I would like to automatically load a file (pdb extension) when rasmol starts. Can anyone help me. thank you very much in advance for your help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Load a file automatically. Date: Mon, 18 Jan 1999 10:59:04 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Depends on what operating system you are using. In Windows, you can make a file rasmol.ini which contains script commands, or calls another script file. See the Reference Manual for unix. I don't know how to do this on Mac. You should probably be using Chime instead. It is designed for presentations, whereas RasMol's great strength is interactive self-directed exploration. When you start trying to get RasMol to do things automatically, you'll find it very limiting -- unlike Chime. At 1/18/99, you wrote: >Hello, > I would like to automatically load a file (pdb extension) when >rasmol starts. Can anyone help me. thank you very much in advance for >your help.& > >James Leong Mook seng >Clairfonds No 2, Vacoas >Mauritius. RasMol Reference Manual: http://www.umass.edu/microbio/rasmol/distrib/rasman.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 Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Rasmol Bonds Date: Mon, 18 Jan 1999 11:11:24 -0800 (PST) To: Rasmol Help Hello, What should I include in the pdb file format to show double and triple bonds in rasmol. Could anyone help me. Thank very much you in advance. If anyone is trying to launch rasmol and loading a pdb file to display from visual c++, i can help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Rasmol Bonds Date: Mon, 18 Jan 1999 11:11:52 -0800 (PST) To: Rasmol Help Hello, What should I include in the pdb file format to show double and triple bonds in rasmol. Could anyone help me. Thank very much you in advance. If anyone is trying to launch rasmol and loading a pdb file to display from visual c++, i can help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Rasmol Bonds Date: Mon, 18 Jan 1999 11:04:28 -0800 (PST) To: Rasmol Help Hello, What should I include in the pdb file format to show double and triple bonds in rasmol. Could anyone help me. Thank very much you in advance. If anyone is trying to launch rasmol and loading a pdb file to display from visual c++, i can help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com Anmar Ali ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: [Fwd: FW: Virus Warning !!] Date: Tue, 19 Jan 1999 16:20:10 +0100 To: "Dr. Jürgen Gauer" , This is a multi-part message in MIME format. --------------2F4FB00959E4758343C7942D --------------2F4FB00959E4758343C7942D Content-Disposition: inline "'Chantal Felten'" , "'Ciaravino Ilda'" , "'Clos Harald'" , "'Deutscher Bernd'" , "'Faller Thomas'" , "'Federico Marcellino'" , "'Fisch Jo'" , "'Frank Grossmann'" , "'Fred Winsmann'" , "'Hafner Thorsten'" , "'Harth Detlev'" , "'Jochen Meister'" , "'Klein Christina'" , "'Lobo'" , "'Lombarski Thorsten'" , "'Loutzoglou Franziska'" , "'Marcellino Federico'" , "Arangio, Mario" , "'Martin Welp'" , "'Massachussets University'" , "'Matheis Joachim'" , "'Meissner Christian'" , "'Miguel'" , "'Odilo'" , "'Poggiolini Alessandra'" , "'Poppi'" , "'Ravagni Alberto'" , "'Ronellenfitsch Enrike'" , "'Schneider Patrick'" , "'Secular L. Donna'" , "'Silvana'" , "'Straub Holger'" , "'Treitz Manfred'" , "'Treitz Manfred home'" , "'Volker Bomm'" , "'Windy'" ++++------+------+------+------+------+------+------+------+------+------+ From: "Arangio, Mario" Subject: FW: Virus Warning !! Date: Tue, 19 Jan 1999 09:44:47 -0500 To: "'Cervone Brunella e Claudio'" , > I was sent this email by a friend of mine. It might not be true, but > be aware just in case. > > Thanks, > Mario > > > > > ---------- > From: Kaplan, Alan > Sent: Tuesday, January 19, 1999 8:22 AM > To: All ArQule Employees > Subject: FW: Virus Warning !! > > > > > > Subject: Virus Warning !! > > > > Just to let you know > > Someone is sending out a very desirable screen-saver, the Budweiser > Frogs > > - > > "BUDDYLST.ZIP". If you download it, you will lose everything!!! > > Your hard drive will crash and someone from the Internet will get > your > > screen name and password! DO NOT DOWNLOAD THIS UNDER ANY > CIRCUMSTANCES!!! > > IT JUST WENT INTO circulation yesterday, as far as we know. Please > > distribute/inform this message. This is a new, very malicious virus > and > > not > > many people know about it. This information was announced yesterday > > morning > > from Microsoft. Please share it with everyone that might access the > > Internet. Once again, pass this along to EVERYONE in your address > book so > > that this may be stopped. Also do not open or even look at any mail > that > > says "RETURNED OR UNABLE TO DELIVER". This virus will attach itself > to > > your > > computer components and render them useless. Immediately delete mail > items > > that say this. AOL has said that this is a very dangerous virus and > that > > there is NO remedy for it at this time. Please practice cautionary > > measures > > and forward this to all your on-line friends ASAP > > > > > > > > --------------2F4FB00959E4758343C7942D Content-Description: Card for Frank Eblinger Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Frank Eblinger n: Eblinger;Frank adr: In den Welkertswiesen 65;;;Saarbrücken;Saarland;66125;Germany email;internet: f.eblinger@rz.uni-sb.de title: Dr. tel;work: 0681-302-3949 tel;fax: 0681-302-4105 tel;home: 06897-764132 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------2F4FB00959E4758343C7942D-- ++++------+------+------+------+------+------+------+------+------+------+ From: Alan Wolfson Subject: Re: [Fwd: FW: Virus Warning !!] Date: Tue, 19 Jan 1999 10:50:00 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, gauer@inm-gmbh.de At 04:20 PM 1/19/99 +0100, Dr. Frank Eblinger wrote: While there may be screen savers containing viruses, that particular one appears to be a hoax. You can easily determine whether it is a hoax or not by doing a little investigation. I assume that most of us here on this list are scientists and are not afraid of doing a little research :-) A quick check of Microsoft's web site (http://www.microsoft.com) did not turn up any virus warning despite the citation in the emailed warning. Here's some information from the Internet Tourbus, a free newsletter that has a lot of useful information in it: ----------- begin included information ----------- To help you combat the sea of urban legends that fills your inbox every day, your fearless bus driver has created the Urban Legend Combat Kit. The Combat Kit is a *FREE* collection of canned email responses that helps you debunk some of the Internet's most prevalent myths and urban legends. Just cut and paste whatever you need. You can find the Combat Kit on my Web site at http://netsquirrel.com/combatkit/ . ----------- end included information ----------- Please make an attempt to verify these type of things before posting them to a list such as this one. Alan Alan Wolfson Senior Consultant MDL Information Systems ++++------+------+------+------+------+------+------+------+------+------+ From: Scot Wherland Subject: Inorganic teaching resources Date: Tue, 19 Jan 1999 08:02:22 -0800 To: rasmol@dhcp-srv2.oit.umass.edu This is an announcement of the enhancement, or at least growth, of my WWW resource page. It is quite a primitive use of Chime, but the collection of structures may be of interest. It has two parts. 1. A periodic table with the elements represented as spheres of their appropriate size. This is viewed with Chime, and has not changed. Note in response to recent posts: I should add a set of vdw radii, but they are hard to find, especially measured ones. 2. A database of experimental structures of about 250 molecules. This has been greatly enlarged through the addition of a number of transition metal complexes showing different coordination numbers and isomers. I now recommend Chime 2 for viewing the structures since it now has the ability to measure bond lengths and angles and is commonly used, but WebLab Viewer is still supported and has advantages. As always, comments and requests are solicited. There is some activity above "background" according to the counter so it appears some use is being made outside the Palouse. I have started extracting subsets of the structures to use in General Chemistry. This is easily done since the structures are individual files. The site is: http://www.wsu.edu/~wherland/ Enjoy, 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: "Marc Bianciotto" Subject: Re: [Fwd: FW: Virus Warning !!] Date: Tue, 19 Jan 1999 17:16:16 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Hi, Be careful about this type of alerts. According to the well-known anti-virus producer Symantec, (I cite) "BUDDYLST.ZIP is not a virus. It is a hoax. The "virus" does not exist. There is currently no virus that has the characteristics ascribed to BUDDYLST.ZIP." I refer to this URL : http://www.symantec.com/avcenter/venc/data/buddylst.zip.html and to this one about hoaxes : http://www.symantec.com/avcenter/hoax.html Go there and see. You have to trust in some people on the Internet, about Rasmol, I trust in this mailing-list, about viruses, I trust in them... Well, this type of message is coming frequently in mailboxes ( Good Times, Penpal Greetings) and it would be quite nice if it wasn't nearly all the time hoaxes like this. Do you know the virus called Paranoia ? Good Rasmol & Chime! Marc Bianciotto *************************************** * Marc Bianciotto * * L.S.P.C.O./I.R.S.A.M.C * * * 118, route de Narbonne * * 1000 Toulouse * * biancio@irsamc1.ups-tlse.fr * *************************************** References: <19990118191124.13425.rocketmail@send102.yahoomail.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: Rasmol Bonds Date: Tue, 19 Jan 1999 10:18:11 -0700 To: rasmol@dhcp-srv2.oit.umass.edu, James Leong Mook seng James, A letter was posted several days ago briefly describing the process necessary to display double bonds in rasmol. First you probably need rasmol 2.6, 2.5 does not show double bonds. Second, if you have a large file it could take awhile since you must manually enter an extra "conect" line for each double bond. The method I am using is convert the pdb file to a MDLmol file, before adding hydrogens. Then checking the structure to verify the double bonds are in the correct place. Sometimes in the conversion the double bonds are not correctly placed, this too is a time consuming process. Then add the hydrogens. Rasmol will show MDLmol files as well as PDB. If I can assist you further send an email. Jeff Ayres James Leong Mook seng wrote: > Hello, > What should I include in the pdb file format to show double and > triple bonds in rasmol. Could anyone help me. Thank very much you in > advance. If anyone is trying to launch rasmol and loading a pdb file > to display from visual c++, i can help.& > > == > > James Leong Mook seng > Clairfonds No 2, Vacoas > Mauritius. > > _________________________________________________________ > DO YOU YAHOO!? > Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Adrian Kornhauser (lab3)" Subject: Re: [Fwd: FW: Virus Warning !!] Date: Tue, 19 Jan 1999 12:12:42 -0600 (CST) To: rasmol@dhcp-srv2.oit.umass.edu Antoher interesting place to "nail" hoaxes is: http://ciac.llnl.gov/ In this particular case the information on the "Bud Frogs Screen Saver" hoax is at: http://ciac.llnl.gov/ciac/CIACHoaxes.html#budfrogs Adrian Kornhauser ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Visitor-maintained index of Chime resources? Date: Tue, 19 Jan 1999 18:45:36 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Dear Chimeleons: Many of you are aware of a page on my site presumptiously titled "World Index: BioMolecular Tutorials in Chime by Subject plus RasMol 'movie' scripts and Chime authoring resources" where 40-some Chime tutorials and resources are indexed and linked (http://www.umass.edu/microbio/rasmol/tutbymol.htm). This project is quite hopeless since time is never available properly to index and link the many new and excellent Chime sites being developed. My apologies to many of you who have pointed out sites to me and got no response. In June, I provided a guestbook so visitors could add their own links and descriptions, but the server we contracted to provide CGI service (not available from the computer center on our campus) has been defunct recently and although a kind colleague has offered us an account at the San Diego Supercomputer Center, we haven't yet installed the guestbook there. In any case, the guestbook contributions are not ideal since they are not indexed and appear on a separate page from the 'World Index'. I think there is a real need for such an index because it is not possible, to my knowledge, to search for pages which invoke Chemscape Chime via Yahoo, Alta Vista, Hotbot, Infoseek, etc. This is because these services (when last I checked) don't index words in tags, so you can't search for .spt or .pdb or application/x-spt or chemical/x-pdb. And of course html files which invoke Chime don't necessarily contain the word Chime, and even the embed tag may be hidden in a separate javascript file which constructs the tag on the fly. If I have missed some trick here, someone please enlighten me! I think the solution is to develop CGI scripts which allow visitors to the World Index to contribute their own index entries and site descriptions with a web form, which will then (after approval by a moderator) be incorporated into a sorted data file, which in turn can be used to regenerate the entire HTML document after every update. This goes beyond the usual guestbook in that the resulting html will contain multiple sections (subject index, author index, and site list with site descriptions) and will always be appropriately alphabetized. Once operational, aside from moderation (approval/rejection/request for revision), the only human effort involved would be on the part of the visitor/contributor. This type of "Visitor-maintained index" is surely needed for areas other than Chime and perhaps someone has already developed code for a different application, in which case I'd love to know about it. We are beginning to plan, and will then code, the PERL required for such a "Visitor-maintained [but moderated to prevent graffiti] index of Chime resources". However we are PERL and CGI novices and it will be a struggle. We would gladly accept assistance from those more experienced should such volunteers wish to come forth! -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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: RE: Visitor-maintained index of Chime resources? Date: Wed, 20 Jan 1999 14:26:22 -0500 To: rasmol@dhcp-srv2.oit.umass.edu David's idea below sounds excellent and I think we should all strive towards it. It would help if MDL would encourage people who write Chime-based resources to use a standard meta-tag, and I'll plan to incorporate it into my template and recommend this elsewhere on my site. Nevertheless I still strongly favor the visitor-maintained index both because there will always be some sites which forget to use these meta-tags, and because a visitor-maintained index with site descriptions written by site authors would be a very useful complement to whole-web searching. -Eric Martz >From: "David Hole" >To: >Subject: RE: Visitor-maintained index of Chime resources? >Or encourage the uniform use of a metatag that would get indexed and would >be easy to search for. Adding a meta tag to most of our pages would be >relatively painless. The key is to get everyone to use the same tag so >searches could be simple. >One possible example would be... > > >David Hole http://wheat.usu.edu/ >Assoc. Professor Utah State University >435-797-2235 dhole@mendel.usu.edu References: <0F5V00GB2HUEUC@rfd1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Re: Visitor-maintained index of Chime resources? Date: Thu, 21 Jan 1999 16:34:40 +0100 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------2892CBFB13FE985FEB23B4E3 Hi to all, 1) For me it's no problem to insert the meta tag in my web sites, but I do not understand how to search for the keywords (.spt, chime...) I tried with altavista: thousands of hits.. 2) Another problem: About 10 days ago I was asking some questions about VdW radii. Did you forget ...? What number does Chime or RasMol use for vdw spacefilling ? 500 is too much, 400 too less.. Does the programm take into account different radii for atoms and ions? Thanks for your help in advance Frank (please visit our web site about supramolecular structures at: http://www.uni-sb.de/matfak/fb11/schneider/supram/supramolecular_structures.html --------------2892CBFB13FE985FEB23B4E3 Content-Description: Card for Frank Eblinger Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Frank Eblinger n: Eblinger;Frank adr: In den Welkertswiesen 65;;;Saarbrücken;Saarland;66125;Germany email;internet: f.eblinger@rz.uni-sb.de title: Dr. tel;work: 0681-302-3949 tel;fax: 0681-302-4105 tel;home: 06897-764132 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------2892CBFB13FE985FEB23B4E3-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Visitor-maintained index of Chime resources? Date: Thu, 21 Jan 1999 11:25:10 -0700 (MST) To: "Dr. Frank Eblinger" Cc: rasmol@dhcp-srv2.oit.umass.edu Hi Frank, > Another problem: About 10 days ago I was asking some questions about > VdW radii. Did you forget ...? What number does Chime or RasMol use > for vdw spacefilling? 500 is too much, 400 too less.. Does the programm > take into account different radii for atoms and ions? The table of Van der Waal's radii used by RasMol can be found in the source code in the file "abstree.h". This file contains a the array "Element" which contains the atomic symbol, the covalent radius, the VdW radius, the CPK colour and the name of each element in the periodic table. For example, carbon has a VdW radius of 387 (1.548 Angstroms), nitrogen of 350 (1.4 Angstroms) and oxygen of 337 (1.348 Angstroms). These are the values used for molecules containing hydrogen atoms. However, most protein structures in PDB do not contain explicit hydrogens as these are not resolved by X-ray crystallography. As a result for molecules without hydrogen atoms, RasMol use "united atom" Van der Waal's radii for carbon, nitrogen, oxygen and sulphur. This is the effective size of an atom plus its hydrogens (commonly used in forcefields and a better approximation of the molecule's surface). These values (also defined in abstree.h) are 468 for carbon (1.872 Angstroms), 375 for nitrogen (1.5 Anstroms) and 350 for oxygen (1.4 Angstroms). Note that the increase for carbon is larger than for oxygen, this is caused by both the average number of aditional hydrogens and how closely they're bound to their parent atom. Unfortunately, RasMol does not maintain a table of ionic radii for each possible charge state of an element, and so the values used by RasMol for displaying salts or similar structures are incorrect. Complete and reliable tables of ionic radii are both rare and harder to encode in computer software. For example, the CRC handbook lists five ionic radii for selenium: -2 (1.91A), -1 (2.32A), +1 (0.66A), +4 (0.50A) and +6 (0.42A). This series fits well with the VdW radius (as used by RasMol) of 0.9A in the uncharged state. One issue is which values should a molecular graphics program use if it doesn't have the required charge state in its tables (Se+2). Each element has an upper bound on its charge, but can theoretically have an arbitrary negative charge. 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 Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id BAA17515 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Debord Subject: Lipophilicity calculation with Chime Date: Fri, 22 Jan 1999 01:37:28 -0500 To: Rasmol List Dear Colleagues, Some time ago I have asked some questions about lipophilicity calculation with Chime. I thank Tim Maffett and Annie Van de Wiele for their replies. With their explanations I was able to modify Eric Martz's command-line demo into a web page which computes the lipophilicity of a molecule and displays its lipophilicity potential. You can download this document from: http://ourworld.compuserve.com/homepages/JDebord/lipophil.zip I hope you will find it useful. Best regards, Jean Debord Laboratoire de Pharmacologie, Faculte de Medecine 2 Rue du Docteur Marcland, 87025 Limoges, France http://ourworld.compuserve.com/homepages/JDebord ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas Gunda" Subject: Re: Rasmol Bonds Date: Fri, 22 Jan 1999 14:00:24 +1 To: rasmol@dhcp-srv2.oit.umass.edu > > James Leong Mook seng wrote: > > > Hello, > > What should I include in the pdb file format to show double and > > triple bonds in rasmol. Could anyone help me. Thank very much you in > > advance. If anyone is trying to launch rasmol and loading a pdb file > > to display from visual c++, i can help.& > > > > == > > > > James Leong Mook seng > > Clairfonds No 2, Vacoas > > Mauritius. > > One possibility is to read the pdb file into e.,g. Mol2mol, add hydrogens, add double bonds, and convert it into an MDL molfile. This MDL molfile will contain the necessary bond order information. 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 ************************************************************************ References: <199901220137_MC2-678E-B0E4@compuserve.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Re: Lipophilicity calculation with Chime Date: Fri, 22 Jan 1999 09:25:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Jean - This does not work for macs. It adds too many /// for the file://// command & thus generates an error. I think Eric Martz fixed a similar problem with his protein explorer. Perhaps you can find out about his solution. Thanks for posting this! Brian Jean Debord wrote: > Dear Colleagues, > > Some time ago I have asked some questions about lipophilicity calculation > with Chime. I thank Tim Maffett and Annie Van de Wiele for their replies. > With their explanations I was able to modify Eric Martz's command-line demo > into a web page which computes the lipophilicity of a molecule and displays > its lipophilicity potential. > > You can download this document from: > > http://ourworld.compuserve.com/homepages/JDebord/lipophil.zip > > I hope you will find it useful. > > Best regards, > > Jean Debord > Laboratoire de Pharmacologie, Faculte de Medecine > 2 Rue du Docteur Marcland, 87025 Limoges, France > http://ourworld.compuserve.com/homepages/JDebord -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ References: <199901220137_MC2-678E-B0E4@compuserve.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Macintosh file://// problem (Lipophilicity site) Date: Fri, 22 Jan 1999 17:34:06 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Re: Jean Debord's lipophilicity Chime site, At 1/22/99, Brian White wrote: >Jean - > This does not work for macs. It adds too many /// for the file://// >command & thus generates an error. I think Eric Martz fixed a similar problem >with his protein explorer. Perhaps you can find out about his solution. >Thanks for posting this! My solution can be seen in full by downloading the protein explorer http://www.umass.edu/microbio/chime/explorer/ The file loading code is in shared\loadit2.js If you seach that file for 'Macintosh' you'll find this nugget: if (pdb_name.substring(0, 7) != "http://" && pdb_name.substring(0, 10) != "../shared/") { if (pdb_name.charAt(0) == "/") // for Macintosh! pdb_name = "file://" + pdb_name; else pdb_name = "file:///" + pdb_name; } You need 3 slashes but for some reason the Netscape browse form slot delivers a prefixed slash on the Mac but not on Windows. In general, I'd suggest that people who want to build Chime sites "from scratch" start with the present protein explorer (and cut out what you don't want) rather than the old "command line demo" which lacks all the refinements I've been adding during the last year as I built the PE. Of course if you wait another week (?) it will have command aliasing, working folder configuration, preferences which survive between sessions, and a few more bug fixes when I release version 0.96. :-) -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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Dr Walter Breau Subject: Protein Explorer JavaScript error Date: Tue, 26 Jan 1999 12:10:55 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Hello, I have been trying to get Protein Explorer to work on my system (Pentium II, 266Mhz, Win95 using Netscape 4.04). I have tried the explorer on Eric's web site and as a download on my harddrive. When I click on the "Load molecule" button I always get the message: JavaScript Error: file///Raswin/Chime2/shared/cookie.js. line 77: test for equality (==) mistype as assignment (=)? Assuming equality test. while (s1 = raw.indexOf ( " ; " , s0) ) .............................................................^ Any suggestions to fix the problem would be appreciated Walter Breau Department of Biology Elms College Chicopee, MA USA 01013 breauw@elms.edu ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: setting a scale Date: Tue, 26 Jan 1999 15:44:45 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Hello. I am using RasMol to generate a series of GIFs of many different molecules. I would like to have all of the molecules displayed at the same scale, but I cannot figure out how to do this. Searching through the FAQs and the user's guide has yielded no satisfactory answer. I have enclosed parts of two posts that are most relevant. If anyone has a possible solution, even an inelegant one, please post it. Thanks. -Aenoch Lynn On Wed, 24 Apr 1996 17:40:28 +0100 (BST), Sayle Dr R A wrote: > Dear Michael, > > 1. Is there a way of setting an absolute scale for a figure? I am > > trying to print different molecules on the same scale for comparison > > purposes. I have tried the ZOOM command but that doesn't seem to work. > > Thanks very much for your email. For a long time, I didn't think that > this was possible but have recently found a bizarre solution. > > The solution is based upon the fact that the maximum "zoom" allowed by > RasMol is dependent upon the size of a molecule. It transpires that for > any molecule the maximum zoom provides an image where 1 Angstrom is equal > to about 128 pixels. > > Hence you load in two molecules, for example "crambin" and "aspirin" into > two different RasMol's. You then determine from the RasMol command line > the maximum allowed zoom parameter. For example, if "zoom 500" reports > "Parameter value too large!", then 500 is too high, otherwise if the (zoom > command is successful) the value is probably too low. > > On my local machine the maximum zoom for "crambin" is 362, and the > maximum scale for "aspirin" is 118. This means that the two images > have the same scale when the ratio of the two zooms is 362:118. > For example, to display "aspirin" on the same scale as the default > "crambin", you should type "zoom 32" into the aspirin window > (and "zoom 100" into the crambin window). On Thu, 17 Oct 1996 22:46:33 -0700, Tim Maffett wrote: > At 12:25 PM 10/17/96 +0100, Andrea Bernini wrote: > >First, thanks to Roger Sayle and Tim Maffett for explanations on write > >command and Chime, now i'm making movies! Now i have two more question > >( i've searched all the manuals and mailing list archives before ask you, > >but find nothing): how can i hide selected atom expression and set the > >work area to a determinate size? > > You can use the 'restrict' command to limit what is displayed. > > I am not sure what you mean you say 'determinate size', but with the > next version of Chime, due out any day now (v 0.99), you can > set the angstroms per inch for a Chime plugin, allowing you to > have several Chime plugins on a page, all displaying molecules in > the same absolute scale. This is currently done with an > tag argument, but I may be adding a rasmol script command for this as > well. X-MSMail-Priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: "Van de Wiele Annie" Subject: are Chime and Rasmol usable with Windows 98 ? Date: Wed, 27 Jan 1999 12:48:10 +0100 To: "rasmol lists" Dear Rasmol Users, Before taking Windows 98, I prefer to know if there is not too much problems with Chime and Rasmol ? My PC is a pentium 233 MMX. Is Window 98 compatible with Chime 2.0 Beta3 ? I have begun a work with Rasmol and as I am a beginner, I do not want to be stopped after because of Windows 98. Thanks to all. Annie I' am working on a mushroom toxin for a french thésis in Lille. Annie Van de Wiele, Pharmacie de la Lys 12 Rue Leon Six, Bousbecque 59166 France tel 0320235267 fax from abroad(00 33)320236234 E.mail :avandewiele@nordnet.fr X-Confirm-reading-to: pacsch@ritvax.isc.rit.edu X-PMrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Paul A. Craig" Subject: Re: are Chime and Rasmol usable with Windows 98 ? Date: Wed, 27 Jan 1999 09:34:31 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Annie: I just switched to WIndows 98 on a Digital computer with a Pentium 233 MMX and have not had any trouble so far. I am running Chime 2.0 full release version. I am using Internet Explorer 4.0 40-bit encryption and Netscape Communicator 4.5 128-bit encryption. Good luck. Paul Craig Date sent: Wed, 27 Jan 1999 12:48:10 +0100 Send reply to: rasmol@lists.umass.edu From: Van de Wiele Annie Subject: are Chime and Rasmol usable with Windows 98 ? To: rasmol lists > Dear Rasmol Users, > > Before taking Windows 98, I prefer to know if there is not too much > problems with Chime and Rasmol ? My PC is a pentium 233 MMX. > Is Window 98 compatible with Chime 2.0 Beta3 ? > I have begun a work with Rasmol and as I am a beginner, I do not want to be > stopped after because of Windows 98. > Thanks to all. > > Annie > > I' am working on a mushroom toxin for a french thésis in Lille. > Annie Van de Wiele, Pharmacie de la Lys > 12 Rue Leon Six, Bousbecque 59166 France > tel 0320235267 fax from abroad(00 33)320236234 > E.mail :avandewiele@nordnet.fr > > Paul A. Craig Phone: 716-475-6145 Rochester Institute of Technology FAX: 716-475-5766 Dept. of Chemistry Lab: 716-475-2495 1 Lomb Memorial Dr. e-mail: pacsch@rit.edu Rochester, NY 14623 WWW: http://www.rit.edu/~pac8612 ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Rasmol bonds Date: Wed, 27 Jan 1999 08:35:37 -0800 (PST) To: Rasmol Help Hello, How can I display double bonds and triple bonds using rasmolv2.5. Thanks a lot in advance for your help. Bye, James == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Protein Explorer JavaScript error Date: Wed, 27 Jan 1999 12:32:54 -0500 To: breauw@elms.edu, rasmol@dhcp-srv2.oit.umass.edu Thanks for reporting this bug, Walter. I have fixed it and when version 0.96 goes on the website the fix will be in it (sometime in the next couple of weeks I hope ...) The bug is harmless, however. If you upgrade to Netscape 4.5, you won't even notice it, because this version doesn't pop javascript errors up in your face like 4.04 and require acknowledgement. I'm not sure that I like this new feature of Netscape 4.5-- its the reason I overlooked the bug! At 1/26/99, you wrote: >Hello, > >I have been trying to get Protein Explorer to work on my system (Pentium >II, 266Mhz, Win95 using Netscape 4.04). I have tried the explorer on >Eric's web site and as a download on my harddrive. When I click on the >"Load molecule" button I always get the message: > >JavaScript Error: file///Raswin/Chime2/shared/cookie.js. line 77: >test for equality (==) mistype as assignment (=)? Assuming equality >test. > > while (s1 = raw.indexOf ( " ; " , s0) ) >.............................................................^ > >Any suggestions to fix the problem would be appreciated > >Walter Breau >Department of Biology >Elms College >Chicopee, MA USA 01013 >breauw@elms.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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <199901262344.PAA20672@socrates.cgl.ucsf.EDU> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: setting a scale Date: Wed, 27 Jan 1999 14:04:21 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Aenoch, Good question. I have noticed if you edit a molecule into several segments, save each of the segments as a .pdb file, then open the save file the scaling changes. If you receive responses please post them. Thanks, Jeff Ayres References: <19990127163537.10061.rocketmail@send102.yahoomail.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: Rasmol bonds Date: Wed, 27 Jan 1999 14:07:48 -0700 To: rasmol@dhcp-srv2.oit.umass.edu James, A letter was posted several days ago briefly describing the process necessary to display double bonds in rasmol. First you probably need rasmol 2.6, 2.5 does not show double bonds. Second, if you have a large file it could take awhile since you must manually enter an extra "conect" line for each double bond. The method I am using is convert the pdb file to a MDLmol file, before adding hydrogens. Then checking the structure to verify the double bonds are in the correct place. Sometimes in the conversion the double bonds are not correctly placed, this too is a time consuming process. Then add the hydrogens. Rasmol will show MDLmol files as well as PDB. If I can assist you further send an email. Jeff Ayres James Leong Mook seng wrote: > Hello, > How can I display double bonds and triple bonds using rasmolv2.5. > Thanks a lot in advance for your help. > > Bye, > James > > == > > James Leong Mook seng > Clairfonds No 2, Vacoas > Mauritius. > > _________________________________________________________ > DO YOU YAHOO!? > Get your free @yahoo.com address at http://mail.yahoo.com X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: I get text instead of chime.... Date: Thu, 28 Jan 1999 14:41:17 -0500 To: rasmol Hi - I've modified some of Eric Martz's pages for my course & I have the following problem. Some pages, when they are loaded into "fresh" netscape (netscape that hasn't seen chime since it was launched) show text instead of the chime frame or the javascript frame. If you go back and forward with netscape's buttons, the problem is fixed & all other loads work fine - until netscape is re-launched. Although it is easily fixed, it scares my computer-phobic students.... This does not happen on all computers - just my all-in-one G3s with netscape 4.5 & chime 2. Does anyone know what's up? How can I fix this? site with this problem: http://intro.bio.umb.edu/111-112/OLLM/111F98/RasPract/RasPract.html thanks! Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ Eric Martz References: <36B0BD5D.4B8DD123@umb.edu> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: I get text instead of chime.... Date: Thu, 28 Jan 1999 15:01:59 +0000 To: brian.white@umb.edu, Rasmol List , Brian White wrote: > Hi - > I've modified some of Eric Martz's pages for my course & I have the > following problem. Some pages, when they are loaded into "fresh" > netscape (netscape that hasn't seen chime since it was launched) show > text instead of the chime frame or the javascript frame. If you go back > and forward with netscape's buttons, the problem is fixed & all other > loads work fine - until netscape is re-launched. Although it is easily > fixed, it scares my computer-phobic students.... > This does not happen on all computers - just my all-in-one G3s with > netscape 4.5 & chime 2. > Does anyone know what's up? How can I fix this? > > site with this problem: > http://intro.bio.umb.edu/111-112/OLLM/111F98/RasPract/RasPract.html > Brian, I just logged onto your site above and was able to view the Chime window fine (I'm on a Mac PowerPC, Chime 2.0a and NS 4.5). However, there were a host of javascript error messages, all reading the same thing: JavaScript Error: http://intro.bio.umb.edu/111-112/OLLM/111F98/RasPract/chim2way.js, line 4: top.control_fr.document.c2w_form has no properties. My guess is that you broke a JS link when you made the modifications, although Eric of course would know better which one. The reason that you see text instead of the Chime window at first may be a result of your NS version: NS 4.5 seems to handle JS errors more subtly than earlier versions. I'm sending this to Eric, too, in case the error message I saw can help him debug it. 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/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: I get text instead of chime.... Date: Tue, 02 Feb 1999 07:52:14 -0500 To: brian.white@umb.edu, rasmol Cc: tdriscoll@amherst.edu I went to the URL you gave (Netscape 4.5, Windows 95). I got the same JS errors Tim reported. "c2w_form" is Chime-2-Way-Form which is the command line slot and message box. JavaScript Error: http://intro.bio.umb.edu/111-112/OLLM/111F98/RasPract/chim2way.js, line 4: top.control_fr.document.c2w_form has no properties. I suspect the errors are because you have eliminated these from your first window, but not your second. I get the errors before pushing the button, as well as more errors after. However, I get no additional errors when going to part II. I looked in the chim2way.js file I have, and line 4 is a comment, so perhaps you (or we?) modified your copy of this file? -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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id IAA05063 ++++------+------+------+------+------+------+------+------+------+------+ From: =?iso-8859-1?Q?=22Dr=2E_Sabine_K=F6pper=22?= Subject: double bonds in xyz files Date: Tue, 2 Feb 1999 14:46:34 +0100 To: "'rasmol@dhcp-srv2.oit.umass.edu'" Hi you all, is it possible to display double or triple bonds in .xyz and multiple .xyz files? The CONECT statement does not work in .xyz, is that correct? Thanks in advance Sabine Köpper ********************************************************* PD Dr. Sabine Köpper Carl v. Ossietzky Universität Oldenburg FB Chemistry P O Box 2503 D-26111 Oldenburg Phone +49 (0) 441-798-3706 FAX +49 (0)441-798 3329 koepper@chemie.uni-oldenburg.de *******************************!!************************ ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: I get text instead of chime.... Date: Tue, 2 Feb 1999 09:53:38 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Has anyone else on this list had netscape 4.06 or later spontaneously lose it's preferences dll's? (you get an error message to reinstall netscape when you try to access your preferences settings). I'm trying to figure out if it's caused by a plugin, and if so, which one. Thank you kindly...... ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Loss of DLL's Date: Wed, 03 Feb 1999 09:39:26 -0500 To: rasmol@dhcp-srv2.oit.umass.edu This happened to me when one of several copies of Netscape (different versions) was "uninstalled" rather than just deleting the files in its specific folder. We simply had to reinstall the current version. At 2/2/99, you wrote: >Has anyone else on this list had netscape 4.06 or later spontaneously lose >it's preferences dll's? (you get an error message to reinstall netscape >when you try to access your preferences settings). I'm trying to figure >out if it's caused by a plugin, and if so, which one. >Thank you kindly...... > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: sprouting hydrogens Date: Wed, 3 Feb 1999 18:14:52 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Cc: lynna@cgl.ucsf.EDU Hello. I am trying to find a program that will be able to place hydrogens onto any molecular structure (in pdb format). The program must run on a linux box (I need the source code) and be able to place hydrogens for not only proteins and nucleic acids, but for other small molecules as well. I ran across references to BABEL, but there were also reports that it did not place hydrogens for modified RNA bases correctly. I also couldn't connect to the URL that I found for BABEL's web site. What do people do to add hydrogens to, say, crystalized structures? What would people suggest? Pointers to web sites or other lists would also be welcome. -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: sprouting hydrogens Date: Wed, 3 Feb 1999 22:35:35 -0500 To: rasmol@dhcp-srv2.oit.umass.edu SwissPdbViewer (version 3.1) sprouts hydrogens. Use Add Hydrogens on the Build menu. SPV is available for Macs and PC's, with SGI version on the way. I have never had any trouble reading SPV's PDB files on other platforms. To get the program, go to http://www.pdb.bnl.gov/expasy/spdbv/mainpage.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 Fax: (207)780-5607 References: <199902040214.SAA23127@socrates.cgl.ucsf.EDU> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: sprouting hydrogens Date: Thu, 04 Feb 1999 14:32:44 +0000 To: rasmol@dhcp-srv2.oit.umass.edu lynna@cgl.ucsf.EDU wrote: > > Hello. > > I am trying to find a program that will be able to place hydrogens > onto any molecular structure (in pdb format). The program must > run on a linux box (I need the source code) and be able to place > hydrogens for not only proteins and nucleic acids, but for other > small molecules as well. I ran across references to BABEL, but > there were also reports that it did not place hydrogens for > modified RNA bases correctly. I also couldn't connect to the URL > that I found for BABEL's web site. > > What do people do to add hydrogens to, say, crystalized structures? > What would people suggest? Pointers to web sites or other lists > would also be welcome. > > -Aenoch Hi, try MolMol at http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ it can add hydrogens to protein structures (I'm not sure about other molecules then proteins). good luck, 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/ pdb-l@pdb.pdb.bnl.gov ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer now has Preferences, Aliases, Projects Date: Thu, 04 Feb 1999 09:54:01 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu, Version 0.96 of my Protein Explorer is now available at http://www.umass.edu/microbio/chime/explorer The Protein Explorer is a RasMol-like interface implemented in Chime. However, the Protein Explorer can offer much greater assistance and automation than is available in RasMol, and Chime version 2's built-in Select Menu is not available in RasMol. The goal of the Protein Explorer is to make visual exploration of protein structure much more accessible to novices, occasional users, or nonspecialists, as well as making it much more convenient than with RasMol, EVEN FOR EXPERTS. Those wishing to explore NMR structures will find the Explorer's model-selection panel especially useful. An alternative form of the Explorer is provided called the Protein Comparator, which allows two molecules to be loaded side by side and manipulated independently, with or without "follow-me" synchronization for mouse-directed movements and zooms. Version 0.96 adds nonvolatile preference settings (such as whether molecules should be spinning immediately after loading), alias expansion with a user-configurable alias list (for example "s l" expands to "select ligand"), and the ability to specify a project folder on your disk for development of command script files. Instructions are provided for how to shorten scripts saved from Chime which, like those saved from RasMol, are usually unnecessarily long and slow to execute. Version 0.96 has not been linked to the UMass Chime Resources site pending provision of a tutorial for those who have no experience with RasMol. For those who have used RasMol, version 0.96 will be straightforward. Its unique features are extensively documented. The Protein Explorer is freely downloadable for local use with or without an Internet connection. Long range plans for the Protein Explorer include building an automated Guide for novices, and integrating it into the Protein Data Bank interface. As usual, I will be especially interested to know if problems occur on Macintoshes, since I have tested this version only on Windows. (On Macintosh Navigator 4.5, the message list keeps focus at the bottom, unlike all other platforms/versions. A preference setting has been provided to add messages to the bottom of the list, rather than the top, so the newest messages will remain in view.) [Further information not repeated here was detailed in the announcement of version 0.95 on January 10, 1999 to this list, viewable at ftp://marlin.bio.umass.edu/pub/shareware/rasmol/email-history ] -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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <199902040214.SAA23127@socrates.cgl.ucsf.EDU> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: sprouting hydrogens Date: Thu, 04 Feb 1999 08:04:35 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Lynn, Many versions of the BABEL program are located at http://ccl.osc.edu/ccl/software.html I was able to download the program several months ago. I am not sure if there is a Linux version. It does sprout hydrogens, however the placement of hydrogens is sometimes incorrect. The errors are hydrogens used in hydrogen bonding between base pairs, and occasionally aromatic hydrogens located on the bases. If you have a large molecule it could require a lot of extra work. Jeff Ayres lynna@cgl.ucsf.EDU wrote: > Hello. > > I am trying to find a program that will be able to place hydrogens > onto any molecular structure (in pdb format). The program must > run on a linux box (I need the source code) and be able to place > hydrogens for not only proteins and nucleic acids, but for other > small molecules as well. I ran across references to BABEL, but > there were also reports that it did not place hydrogens for > modified RNA bases correctly. I also couldn't connect to the URL > that I found for BABEL's web site. > > What do people do to add hydrogens to, say, crystalized structures? > What would people suggest? Pointers to web sites or other lists > would also be welcome. > > -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Protein Explorer now has Preferences, Aliases, Projects Date: Thu, 4 Feb 1999 10:05:46 -0500 To: rasmol@dhcp-srv2.oit.umass.edu >Version 0.96 has not been linked to the UMass Chime Resources site pending >provision of a tutorial for those who have no experience with RasMol. For >those who have used RasMol, version 0.96 will be straightforward. Its >unique features are extensively documented. In the meantime, my RasMol Tutorial might be useful to beginnners who want to use Protein Explorer. See http://macweb.acs.usm.maine.edu/chemistry/GR/GraphicsGallery/RasTut.html I am hoping to find time to adapt this tutorial for Protein Explorer, once I see from "customer" response that the whole package is reliable on Macs. Maybe by summer. 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 Fax: (207)780-5607 References: <199902040214.SAA23127@socrates.cgl.ucsf.EDU> <36B9B703.1D0D6B01@ycpo.yavapai.cc.az.us> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: sprouting hydrogens Date: Thu, 04 Feb 1999 10:37:02 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu "Jeffrey J. Ayres" wrote: > Lynn, > Many versions of the BABEL program are located at > http://ccl.osc.edu/ccl/software.html > I was able to download the program several months ago. I am not sure if > there is a Linux version. It does sprout hydrogens, however the > placement of hydrogens is sometimes incorrect. The errors are hydrogens > used in hydrogen bonding between base pairs, and occasionally aromatic > hydrogens located on the bases. If you have a large molecule it could > require a lot of extra work. > > Jeff Ayres Unfortunately, this link is not functional at the moment (I just tried it and found a message in the README that says it's "under development"). Any other suggestions where to check out BABEL? 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/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: sprouting hydrogens Date: Thu, 04 Feb 1999 11:05:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu

Date: Thu, 4 Feb 1999 10:39:31 +0200 (IST)

MOLMOL, this program runs on a linux, PC, UNIX workstation,
but complicated enough.
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

Elena.

From: sinvae@mail.biu.ac.il
References: <199902040214.SAA23127@socrates.cgl.ucsf.EDU> ++++------+------+------+------+------+------+------+------+------+------+ From: James Milner-White Subject: Chime on iMacs Date: Thu, 4 Feb 1999 16:59:24 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Has anyone experience of using Chime2.0a on iMacs? We had lots of problems on older Macs but maybe iMacs are better? James Milner-White Dr E. James Milner-White Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G128QQ, UK. E-mail: E.J.Milner-White@bio.gla.ac.uk FAX: +44(0)141-330-4620 Tel.: +44(0)141-330-5283 Research Interests: http://www.enzyme.gla.ac.uk/Biostructures/discoveries.html http://www.biochem.gla.ac.uk/BMB/Res/BSA/EJM.html Teaching Interests: http://www.enzyme.gla.ac.uk/Biostructures/teaching.html ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Big scripts crash RasMac Date: Thu, 04 Feb 1999 19:08:34 +0200 To: RasMol list , info@rcsb.org A simple search interface has been released by the new PDB (www.rcsb.org). For each structure there is a 'Geometry' check, from which a "Fold Deviation Score' can be seen graphically with RasMol. This is a very easy way to see which parts of a structure deviate in bond lengths and angles from standard. I've tested RasMol on UNIX, Windows and Macintosh, and all are fine for small structures (less that 100 residues), but for large structure these scripts crash the Mac (even if you assign it a large amount of memory) - tested on Mac powerbook G3/OS 8.1/Netscape 4.5 Do other people suffer the same problem? Can anyone think of another way around this? 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: jayres@ycpo.yavapai.cc.az.us Subject: Re: sprouting hydrogens Date: Thu, 4 Feb 1999 10:26:09 PDT To: tdriscoll@amherst.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Hello again, An alternative address for the Babelwin program is from Dr. Jeffrey Gosper's Home Page at Brunel University. http://www.brunel.ac.uk/depts/chem/ch241s/re_view/tagon.htm It is an active link. Jeff Ayres ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Big scripts crash RasMac Date: Thu, 04 Feb 1999 19:25:25 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Redirected for Helge Weissig to circumvent technical difficulties: >Date: Thu, 4 Feb 1999 10:57:27 -0800 >From: Helge Weissig >To: Kurt Giles >cc: RasMol list , info@rcsb.org >Subject: Re: Big scripts crash RasMac > >Dear Kurt, > > I am a Mac person myself and I, unfortunately, can only report the >same problems. In fact, I have never been able to make any Mac run RasMac >with a script, not even small ones. > >We decided to release the Structure Explorer pages including the script >producing features nevertheless because a majority of users connects from >different platforms. I am very open to any suggestions as to how we can >warn Macintosh people *subtely* about the restrictions. > >Chime as an alternative would actually be most desireable! Unfortunately, >vs. 2.0 of the plugin does not fare well (at least in our hands) on the >Macs either. > >best, >h. > >+--------------------------------------------+ >| Helge Weissig | >| Project Manager, Structural Bioinformatics | >| San Diego Supercomputer Center +-----------------------------------+ >| voice: +1 619 534 8399 | mail: PO Box 85608 | >| fax: +1 619 822 0873 | San Diego, CA 92186-5608 | >+---------------------------------| direct: 10100 John J. Hopkins Dr. | > | La Jolla, CA 92093-0537 | > +-----------------------------------+ > > > > >On Thu, 4 Feb 1999, Kurt Giles wrote: > >> A simple search interface has been released by the new PDB (www.rcsb.org). >> >> For each structure there is a 'Geometry' check, from which a "Fold Deviation >> Score' can be seen graphically with RasMol. >> This is a very easy way to see which parts of a structure deviate in bond >> lengths and angles from standard. >> I've tested RasMol on UNIX, Windows and Macintosh, and all are fine for >> small structures (less that 100 residues), but for large structure these >> scripts crash the Mac (even if you assign it a large amount of memory) - >> tested on Mac powerbook G3/OS 8.1/Netscape 4.5 >> Do other people suffer the same problem? Can anyone think of another way >> around this? >> >> 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Steven Verhey Subject: Re: Big scripts crash RasMac Date: Thu, 4 Feb 1999 17:23:39 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu I'm a little confused by all these mac problems. I've used scripts extensively both with my PPC6500 (Netscape 4.5, Chime 2.0, Rasmol 2.6) and with various Powerbooks. At home, I have an iMac that runs Chime just fine (I haven't tried scripts there). And when I go to www.rcsb.org, get 2hhb, and choose geometry/fold deviation score I get something that I don't understand, but that doesn't crash my computer. Steve Verhey The Evergreen State College On Thu, 4 Feb 1999, Eric Martz wrote: > Redirected for Helge Weissig to circumvent technical difficulties: > > >Date: Thu, 4 Feb 1999 10:57:27 -0800 > >From: Helge Weissig > >To: Kurt Giles > >cc: RasMol list , info@rcsb.org > >Subject: Re: Big scripts crash RasMac > > > >Dear Kurt, > > > > I am a Mac person myself and I, unfortunately, can only report the > >same problems. In fact, I have never been able to make any Mac run RasMac > >with a script, not even small ones. > > > >We decided to release the Structure Explorer pages including the script > >producing features nevertheless because a majority of users connects from > >different platforms. I am very open to any suggestions as to how we can > >warn Macintosh people *subtely* about the restrictions. > > > >Chime as an alternative would actually be most desireable! Unfortunately, > >vs. 2.0 of the plugin does not fare well (at least in our hands) on the > >Macs either. > > > >best, > >h. > > > >+--------------------------------------------+ > >| Helge Weissig | > >| Project Manager, Structural Bioinformatics | > >| San Diego Supercomputer Center +-----------------------------------+ > >| voice: +1 619 534 8399 | mail: PO Box 85608 | > >| fax: +1 619 822 0873 | San Diego, CA 92186-5608 | > >+---------------------------------| direct: 10100 John J. Hopkins Dr. | > > | La Jolla, CA 92093-0537 | > > +-----------------------------------+ > > > > > > > > > >On Thu, 4 Feb 1999, Kurt Giles wrote: > > > >> A simple search interface has been released by the new PDB (www.rcsb.org). > > >> > >> For each structure there is a 'Geometry' check, from which a "Fold > Deviation > >> Score' can be seen graphically with RasMol. > >> This is a very easy way to see which parts of a structure deviate in bond > >> lengths and angles from standard. > >> I've tested RasMol on UNIX, Windows and Macintosh, and all are fine for > >> small structures (less that 100 residues), but for large structure these > >> scripts crash the Mac (even if you assign it a large amount of memory) - > >> tested on Mac powerbook G3/OS 8.1/Netscape 4.5 > >> Do other people suffer the same problem? Can anyone think of another way > >> around this? > >> > >> 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 > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > RasMol list References: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Running scripts on RasMac Date: Fri, 05 Feb 1999 13:24:10 +0200 To: Helge Weissig , Cc: info@rcsb.org > I am a Mac person myself and I, unfortunately, can only report the > same problems. In fact, I have never been able to make any Mac run RasMac > with a script, not even small ones. > > We decided to release the Structure Explorer pages including the script > producing features nevertheless because a majority of users connects from > different platforms. I am very open to any suggestions as to how we can > warn Macintosh people *subtely* about the restrictions. The trick to running scripts on RasMac is to edit the MIME type so that the File Type is RSML and not TEXT. See http://www.pdb.bnl.gov/pdb-docs/Mac_conf.html (or the equivalent page from your local PDB mirror) 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: Subject: Re: Running scripts on RasMac Date: Fri, 5 Feb 1999 11:38:35 +0000 (GMT) To: rasmol@dhcp-srv2.oit.umass.edu Kurt, > The trick to running scripts on RasMac is to edit the MIME type so that the > File Type is RSML and not TEXT. > > See http://www.pdb.bnl.gov/pdb-docs/Mac_conf.html > (or the equivalent page from your local PDB mirror) I too have problems running RasMol scripts from a web-page on my Mac. This is definitely the way to get RasMac to recognize the file as a script, but it also causes my Mac to crash. Any more ideas anyone? (PowerBook 5300cs, 7.5.3, NS3.04, RasMac 2.6) 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: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: Big scripts crash RasMac Date: Fri, 05 Feb 1999 14:28:13 +0200 To: Steven Verhey Cc: rasmol@dhcp-srv2.oit.umass.edu Steven Verhey wrote: > > I'm a little confused by all these mac problems. I've used scripts > extensively both with my PPC6500 (Netscape 4.5, Chime 2.0, Rasmol 2.6) > and with various Powerbooks. At home, I have an iMac that runs Chime > just fine (I haven't tried scripts there). And when I go to > www.rcsb.org, get 2hhb, and choose geometry/fold deviation score I get > something that I don't understand, but that doesn't crash my computer. The 'Fold Deviation Score' link for 2hhb crashes my machine (Powerbook G3/OS 8.1/Netscape 4.5) as soon as it starts up RasMac. I tried reinstalling RasMac, first from the PDB, then from Eric Martz's site, and the same happened both times (at University of Edinburgh, I couldn't get into v2.6beta folder for some reason). Can you remember where you downloaded your version from? Is it 2.6b2a you're using (i.e. does stereo work OK)? Smaller files, such as 1HUP are fine on 'Fold Deviation Score' with RasMac - the crashing only occurs with bigger structures. 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: Kurt Giles Subject: RacMac crashing problem solved (maybe) Date: Fri, 05 Feb 1999 14:44:24 +0200 To: RasMol list I think I understand the RasMac crashing problem - it may be to do with the type of line feed/carriage return used. The fds-cgi file sent from the "Fold Deviation Score" link is a script followed by the (CA only) PDB file. Looking at this file in a text editor (BBEdit Lite), the script is OK, but the PDB file is one long line. For smaller PDB files RasMac can still manage, but for bigger files this line is too long and RasMac crashes (at least for some of us). 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: Steven Verhey Subject: Re: Big scripts crash RasMac Date: Fri, 5 Feb 1999 09:40:59 -0800 (PST) To: Kurt Giles Cc: rasmol@dhcp-srv2.oit.umass.edu I got my Rasmac from Eric Martz's site, and stereo works fine. FDS sends a file called fds.cgi. It's when I open that with Rasmac that I get something I don't understand, but no crash. Reading the script, I don't think I'm seeing what I'm supposed to be seeing. What I see is the four heme groups in wireframe/cpk, and nothing else. There's more to be seen by running the menus, but only the heme groups show on opening. Steve On Fri, 5 Feb 1999, Kurt Giles wrote: > Steven Verhey wrote: > > > > I'm a little confused by all these mac problems. I've used scripts > > extensively both with my PPC6500 (Netscape 4.5, Chime 2.0, Rasmol 2.6) > > and with various Powerbooks. At home, I have an iMac that runs Chime > > just fine (I haven't tried scripts there). And when I go to > > www.rcsb.org, get 2hhb, and choose geometry/fold deviation score I get > > something that I don't understand, but that doesn't crash my computer. > > The 'Fold Deviation Score' link for 2hhb crashes my machine (Powerbook G3/OS > 8.1/Netscape 4.5) as soon as it starts up RasMac. I tried reinstalling > RasMac, first from the PDB, then from Eric Martz's site, and the same > happened both times (at University of Edinburgh, I couldn't get into > v2.6beta folder for some reason). > Can you remember where you downloaded your version from? Is it 2.6b2a you're > using (i.e. does stereo work OK)? > > Smaller files, such as 1HUP are fine on 'Fold Deviation Score' with RasMac - > the crashing only occurs with bigger structures. > > > 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: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: Big scripts crash RasMac Date: Fri, 05 Feb 1999 20:03:44 +0200 To: Steven Verhey Cc: rasmol@dhcp-srv2.oit.umass.edu Steven Verhey wrote: > > I got my Rasmac from Eric Martz's site, and stereo works fine. FDS > sends a file called fds.cgi. It's when I open that with Rasmac that I get > something I don't understand, but no crash. Reading the script, I don't > think I'm seeing what I'm supposed to be seeing. What I see is the four > heme groups in wireframe/cpk, and nothing else. There's more to be seen > by running the menus, but only the heme groups show on opening. No, you're not getting what you're supposed to be seeing: you should get a 'backbone' representation of the structure coloured by it's deviation from 'normal' bond lengths and angles (blue is OK, varying up to red which is very unusual lengths/angles). It sounds as if you don't have the 'File Type' on your MIME type set to RSML. Doing this, you will read the scripts properly (but be warned, it will probably crash with large PDB files, try something small first). It appears the problem is with the size of the PDB file and not the script: see my mail "RacMac crashing problem solved (maybe)" from 12.44 GMT. 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: Steven Verhey Subject: Re: Big scripts crash RasMac Date: Fri, 5 Feb 1999 11:19:11 -0800 (PST) To: Kurt Giles Cc: rasmol@dhcp-srv2.oit.umass.edu Cool! I've succeeded in getting my mac to crash! After making the MIME change you suggest, FDS results in a bomb ("Error in 'Finder' of Type 10" or something like that). I haven't tried smaller files, but I accept your diagnosis of the problem. Unfortunately, I seem to have lost your "Rasmac crashing problem solved (maybe)" e-mail. Could you resend it to me offlist? Steve On Fri, 5 Feb 1999, Kurt Giles wrote: > Steven Verhey wrote: > > > > I got my Rasmac from Eric Martz's site, and stereo works fine. FDS > > sends a file called fds.cgi. It's when I open that with Rasmac that I get > > something I don't understand, but no crash. Reading the script, I don't > > think I'm seeing what I'm supposed to be seeing. What I see is the four > > heme groups in wireframe/cpk, and nothing else. There's more to be seen > > by running the menus, but only the heme groups show on opening. > > No, you're not getting what you're supposed to be seeing: you should get a > 'backbone' representation of the structure coloured by it's deviation from > 'normal' bond lengths and angles (blue is OK, varying up to red which is > very unusual lengths/angles). > > It sounds as if you don't have the 'File Type' on your MIME type set to > RSML. Doing this, you will read the scripts properly (but be warned, it will > probably crash with large PDB files, try something small first). > It appears the problem is with the size of the PDB file and not the script: > see my mail "RacMac crashing problem solved (maybe)" from 12.44 GMT. > > > 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: James Leong Mook seng Subject: Rasmol Bonds Date: Fri, 5 Feb 1999 13:30:14 -0800 (PST) To: Rasmol Help Hello, Could anyone please tell me how to represent double and triple bonds using rasmolv2.5.thank you very much in advance. I have try the CONECT but it does not work. May be i had not used it correctly,could anyone help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: RasMac crashing problem/RasMac 2.6.4 Date: Mon, 08 Feb 1999 11:58:23 +0200 To: RasMol list The RasMac crashing problem (it indeed turned out to be a script size problem and not a line feed/carriage return problem), as dicussed over the last week, is a bug in version 2.6b2. This is the version available at Eric Martz's site and through the (Brookhaven) PDB mirror sites. Version 2.6.4 of RasMac (containing minor bug fixes, and overcoming the crashing problem), is available at ftp://ftp.dcs.ed.ac.uk/pub/rasmol/rasmac.sit.hqx or http://inn-prot.weizmann.ac.il/download/rasmac.sit.hqx 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: Kurt Giles Subject: Don't download RasMac 2.6.4 (yet) Date: Mon, 08 Feb 1999 13:39:30 +0200 To: RasMol list Although 2.6.4 lets you look at the very nice 'Fold Deviation Score' from the new PDB, it has a more serious problem of not letting you look at the standard structures from the new PDB, old PDB, SCOP etc. 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: Subject: Re: RasMac crashing problem/RasMac 2.6.4 Date: Mon, 8 Feb 1999 11:46:59 +0000 (GMT) To: rasmol@dhcp-srv2.oit.umass.edu Dear List, Kurt Giles wrote: > > The RasMac crashing problem (it indeed turned out to be a script size > problem and not a line feed/carriage return problem), as dicussed over the > last week, is a bug in version 2.6b2. This is the version available at Eric > Martz's site and through the (Brookhaven) PDB mirror sites. > > Version 2.6.4 of RasMac (containing minor bug fixes, and overcoming the > crashing problem), is available at > > ftp://ftp.dcs.ed.ac.uk/pub/rasmol/rasmac.sit.hqx > > or > > http://inn-prot.weizmann.ac.il/download/rasmac.sit.hqx and indeed my Mac now doesn't crash when I attempt to run a script. However, when I use RasMac as a helper to Netscape, I now get (from RasMac) the error message: "", line 1: Script command line too long! Which looks as if it *could* be a CR/LF translation problem. The web-server I am trying to download from (which is also mine, and uses httpd) is a UNIX machine, and UNIX uses just LFs to mark end-of-line. Can anyone tell me: (a) What the Mac uses for EOL? (is it just CR?) (b) How to tell either Netscape on the Mac, or httpd on the server to do the appropriate translation? 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: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: RasMac crashing problem/RasMac 2.6.4 Date: Mon, 08 Feb 1999 15:15:28 +0200 To: RasMol list > > and indeed my Mac now doesn't crash when I attempt to run a script. However, > when I use RasMac as a helper to Netscape, I now get (from RasMac) the error > message: > > "", line 1: Script command line too long! > > Which looks as if it *could* be a CR/LF translation problem. The > web-server I am trying to download from (which is also mine, and uses > httpd) is a UNIX machine, and UNIX uses just LFs to mark end-of-line. > Yes, I discovered the same problem (hence the later warning not to get 2.6.4), but I don't think this is a CR/LF problem, and so can't be solved with a simple translation. As far as I can work out, the difference between the following scripts: http://www.rcsb.org/pdb/cgi/render.cgi/1IGD.pdb?pdbId=1IGD&format=rasmol_default http://www.rcsb.org/pdb/cgi/fds.cgi?id=1IGD is that the first starts: load pdb inline exit whereas the second, starts with the same line, but has a number of commands before the exit. The first one cause the problem you describe, but the second work OK. Kurt boundary="----_=_NextPart_001_01BE537C.B8E88990" ++++------+------+------+------+------+------+------+------+------+------+ From: Morgan Ryan Subject: Rasmac 24 bit--anyone got one? Date: Mon, 8 Feb 1999 11:11:44 -0500 To: "'rasmol@lists.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_01BE537C.B8E88990 Does anyone has a Rasmac 2.6 complied for 24-bit version that they could email me? I had one long ago but it has disappeared. And I have no access to a compiler, and I'm too simple to figure out how to do the compile myself using the freeware compiler from Apple. A url or an email would be greatly appreciated. Morgan Ryan mryan@worthpub.com ------_=_NextPart_001_01BE537C.B8E88990 Rasmac 24 bit--anyone got one?

Does anyone has a Rasmac 2.6 = complied for 24-bit version that they could email me? I had one long = ago but it has disappeared. And I have no access to a compiler, and I'm = too simple to figure out how to do the compile myself using the = freeware compiler from Apple. A url or an email would be greatly = appreciated.

Morgan Ryan = mryan@worthpub.com

------_=_NextPart_001_01BE537C.B8E88990-- ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: Re: RasMac crashing problem/RasMac 2.6.4 Date: Mon, 8 Feb 1999 17:12:45 +0000 (GMT) To: rasmol@dhcp-srv2.oit.umass.edu Kurt Giles wrote: > As far as I can work out, the difference between the following scripts: > > http://www.rcsb.org/pdb/cgi/render.cgi/1IGD.pdb?pdbId=1IGD&format=rasmol_default > > http://www.rcsb.org/pdb/cgi/fds.cgi?id=1IGD > > is that the first starts: > > load pdb inline > exit > > whereas the second, starts with the same line, but has a number of commands > before the exit. > The first one cause the problem you describe, but the second work OK. I have just used Netscape to download those files to my UNIX machine (i.e. not passing them to rasmol for interpretation) and looked at them with od. The big difference, other than the one you point out, is that ends of lines in http://www.rcsb.org/pdb/cgi/fds.cgi?id=1IGD are marked by just a newline (octal 012) character (which is the UNIX-style), but http://www.rcsb.org/pdb/cgi/render.cgi/1IGD.pdb?pdbId=1IGD&format=rasmol_default uses a carriage-return;newline (carriage-return is octal 015) pair (which is the DOS-style). >From the behaviour, this is the opposite to what I'd expect if the problem was indeed end-of-line translations, so I'm not sure where this all gets us! 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: Eric Martz Subject: gzipping on a Mac? Date: Tue, 09 Feb 1999 13:39:16 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Does anyone know how to gzip a PDB file on a Macintosh so Chime can read it? (For those who don't have access to a Windows machine) -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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <199902091836.NAA07720@marlin.bio.umass.edu> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: gzipping on a Mac? Date: Tue, 09 Feb 1999 14:20:57 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Eric Martz wrote: > Does anyone know how to gzip a PDB file on a Macintosh so Chime can read > it? (For those who don't have access to a Windows machine) > > -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 > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ I have a straightforward program called ZipIt (shareware; $15) which seems to work great: I can zip and unzip files with no problem. But is there a secret to viewing zipped files with Chime? A zipped pdb appears to load into the Protein Explorer just fine, for example, but no structure shows up, and neither th