++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Saving rotated PDB files Date: Thu, 01 Jan 1998 12:10:30 -0500 To: rasmol@dhcp-srv2.oit.umass.edu On Dec 26 I announced a comparison of the PDB editing capabilities and limitations of RasMol, Chime and Weblab at http://www.umass.edu/microbio/rasmol/pdbtools.htm Nicolas Guex has now kindly provided information for his Swiss-PDBViewer. The good news is that it can save ROTATED AND TRANSLATED COORDINATES WITH ORIGIN OF USER CENTER, and that is controlled by disabling a menu option 'Save in original orientation'. You can save selected residues (evidently not atom by atom selections?) as well. Further details have been added to the above web page. Among the packages compared, this is currently the only freeware with such capabilities. Earlier parts of this thread on our list are on Dec 14 and Dec 15 as well as Dec 26. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Nav4.04 SOLUTION! Absolute javascript references needed. Date: Thu, 01 Jan 1998 13:17:19 -0500 To: rasmol@dhcp-srv2.oit.umass.edu On Dec 30 I reported here that some of my Chime web sites which work under Win95 with Chime 1.0/2.0beta1 Navigator 4.01 fail under Navigator 4.04. Bryan van Vliet of MDL was kind enough to track down the problem and come up with a solution. It appears that Nav4.04 is less forgiving about javascript references in a multi-frame page. Whether this might be relaxed in Nav4.05 (not yet available) is unclear. Although the embed tag which invokes Chime in my code is in the same frame as the javascript include which defines the messagecallback function, Nav4.04 requires that the frame where the function is defined be explicit ('absolute'). So, my invocation fails to allow messages to reach ChimeMsg(), javascript reporting that ChimeMsg() is undefined. Changing the last line above to MessageCallback="top.fr_chime.ChimeMsg"> works! (Thanks to Bryan!) 'top' is a generic reference to the top level of the current window. 'fr_chime' is the name I assigned (in the frameset) to the frame which contains in its header where the function ChimeMsg() is defined. Despite the fact that it is the same frame containing the , Nav4.04 requires an absolute reference. This explains why my 'command line interface demonstration' http://www.umass.edu/microbio/chime/chimehow/fs_cmdln.htm fails to work in Nav4.04 but works in Nav4.01. Maybe soon I'll fix it, or maybe Nav4.05 will fix it .... In any case, these absolute references are probably a good idea. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Changing the subject to a related issue, I was recently working on a presentation in which the contents of any one of the three frames I was using can change. This created the problem that javascript functions and variables needed to maintain state disappeared when the frame which defined them loaded a new document. After staring at the javascript reference manual for awhile http://developer.netscape.com/library/documentation/communicator/jsref/index .htm I stumbled upon the following solution. The javascript functions and variables must be defined in the header of the frameset! (Rather than in the header of a particular document to be loaded into one frame.) Then they remain available regardless of what documents are in any particular frames. The minor catch is that you must reference the variables and functions with absolute references (sound familiar?). For example, if your javascript contains var user_option1 = 0; function apply_options() { // do something controlled by user_option1 } and that javascript file is included in the header of the FRAMESET file then in any one of the frame documents, you could set user_option1 with top.user_option1 = 1; and call apply_options() with parent.apply_options(); ('parent' and 'top' are synonomous as far as I know: top level of the current window, or parent of the current frame.) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ Molmol ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Molecular Dynamics Date: Fri, 02 Jan 1998 00:29:16 +0100 To: Rasmol Mailinglist , Hi all, for validation of a molecular dynamics approach we need a well known, small protein molecule which should be available in PDB- or other common macromolecule-structure-format from both diffraction and NMR-data with good resolution. NMR-data needs to be in multiple-conformation-format (PDB: model1, model2, [..]). We have thought about using Lysozyme because this is one of the best known proteins. Unfortunately there seems only one entry in the PDB-archive derived from NMR-data. We will continue to crosscheck for other entries, but maybe someone has allready done a similar task and might want to help us! If someone knows another molecule which might fullfill the requirements listed above, please email! Thanks in advance. ------------------------------------------------------------------------ Disclaimer: Due to the fact, that this message will be crossposted to several groups and lists, I have to write in english (sorry, hope it does not offend anyone in the local echos). -- Bye, Marc Saric Lehrstuhl für Biophysik Ruhr-Universität Bochum ++++------+------+------+------+------+------+------+------+------+------+ From: Derk Andrew Wierda Subject: Re: Chime problem/Navigator 4.03 Date: Fri, 2 Jan 1998 11:12:48 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Hi all, I tried the page with Netscape 3.02 (gold) and it worked and with 4.03 (pro) and it locked up my Mac. Hope this helps. Derk Wierda >Dear Chimers, > >This is a follow up to my previous message about a Chime problem with >Navigator 4.03. > >If you try to open the url from my original message, listed below, you will >get a "File not found" error message. I think the error message is >misleading. The page does exist at that address, but the same error that >causes crashes blocks us from opening it. Another way to see it is to go to > > >http://www.mdli.com/chemscape/chime/chime.html > >which loads without problem. Then scroll down to and click on... > >> Sample page - Test your Chime installation with the following sample page > > >That should cause a Netscape crash. > >So far two people have responded to my original message & both got the >error message. It looks like it is a real browser problem and not something >just in my machine. > >Hopefully, MDLI has some advice. > >Harry > >Previous message: > >We have encountered a problem that occurs with Netscape Navigator 4.03 on >the Macintosh on pages with multiple Chime models. We have a page with 16 >models in small windows. When we open it into a Netscape window large >enough so that all the models can fit, every thing is OK. When we open it >into a smaller Netscape window, so that one line of models is off the >screen, Netscape always crashes. > >We tested this at the MDL site, by trying to open > >http://www.mdli.com/chemscape/example/sample/sample.html > >It crashed Netscape every time. > >When we were using various Navigator 3.0x browsers this did not happen so >we suspect that it's something in the newer browser. > >Limited testing with a Windows95 machine showed no problems there. > >If you have Netscape Navigator 4.03 on a Macintosh would you test the mdli >page mentioned above and let us know what happens. > >If you're at MDL please let us know what you think. Should we continue to >stick with and recommend Navigator 3.0x? > >Harry Ungar haungar@cruzio.com >C4: Computers in Chemistry at Cabrillo College >6500 Soquel Dr. Aptos, CA 95003 >408-479-5059 >http://c4.cabrillo.cc.ca.us _______________________________________________________ Derk Andrew Wierda Phone: (603) 641-7148 Department of Chemistry Fax: (603) 641-7116 100 Saint Anselm Drive dwierda@anselm.edu Manchester, New Hampshire 03102-1310 ++++------+------+------+------+------+------+------+------+------+------+ From: bryan@mdli.com (Bryan Van Vliet) (by way of Eric Martz ) Subject: Chime(tm) / Chime Pro(tm) 2.0 Beta 2 Now Available Date: Sat, 03 Jan 1998 21:27:35 -0500 To: rasmol@dhcp-srv2.oit.umass.edu MDL Information Systems, Inc. has posted Chime 2.0 Beta 2 for Windows 95/NT at http://www.mdli.com/download/chime or http://www.mdli.co.uk/download/chime. Highlights: + Printing now works properly from Navigator 3.04. Netscape has told us they will fix printing of plug-ins in Communicator 4.05 (not yet available.) We are working on printing issues with Internet Explorer. + The Chime installer now registers the required file types so that Internet Explorer can access local files. + Chime 2.0 Beta 2 can now properly hot-link multiple structures into Sculpt to, for example, allow overlay of results from a database search. See http://www.intsim.com/chime.html for more details about Sculpt and the Chime integration. We are working on a Macintosh version of Chime 2.0. We are also planning to provide an SGI version. We are not planning to port Chime 2.0 to Windows 3.1 for the following reasons: the Windows 3.1 user base is shrinking quickly; the port to Windows 3.1 is not straightforward due to differences between 32-bit and 16-bit architectures; the web browser support for Windows 3.1 is "challenging" to say the least; 32-bit Windows is a superior architecture; and the advent of sub-$1000.00 Pentium machines really does provide a reasonable upgrade path to 32-bit technology. Please read the Release Notes before downloading Chime 2.0. Once you have installed Chime 2.0, please try the demonstrations. Bryan Van Vliet Director, Internet Technologies MDL Information Systems, Inc. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime 2 beta 2 is IMPRESSIVE! Date: Sat, 03 Jan 1998 22:29:23 -0500 To: rasmol@dhcp-srv2.oit.umass.edu For those who haven't taken a look and are curious, Chime 2 (now available for beta-test v2 for Win95 only) has some very impressive new features not mentioned in Bryan van Vliet's announcement which just preceded this message. Many of these can be seen by viewing the demonstration pages provided at MDL's site, http://www.mdli.com/download/chime/ Here are some that I especially like. MENUS are greatly enhanced: The most dramatic menu change is a new 'Select' menu. It allows selection by atom, residue, chain, or model (submenus list all present in the loaded structure!), or selection of protein, dna, backbone, solvent or non-solvent, ligand, non-hydrogen, or predefined terms such as 'hydrophobic', 'pyrimidine' etc. etc. (all on a menu!). From the Select menu, you can change a mouse-click from merely identifying an atom to selecting atoms, bonds, chains, or residues. Moreover, the 'Modify selection mode' menu allows newly selected items to be added to or subtracted from the currently selected set (and other Boolean options)! 'Highlight selection' makes all selected atoms orange, so it is easy to see what you're doing. And there are menu options to 'hide selected' or 'invert selection'. Also on the Select menu is a 'Change color to' menu which lists 13 colors (this list may be expanded in a future release since Chime now recognizes, at command level, over 100 Navigator color names). The 'amino' color scheme (always available from the command line) is now on the Color Menu. It is preferred by some to the Shapely color scheme which has always been on the menu. Edit, Copy Chime Script now places on the clipboard (ready to be saved to a file e.g. by Wordpad -- as PLAIN TEXT) a RasMol-style script which will play back to regenerate the image present when it was saved. This script is superior to what RasMol 2.6 beta2a will save in several respects (it remembers the selected subset of atoms, defined tokens, and the center of rotation, unlike RasMol; and hopefully soon it will fix the non-black background bug). This script also includes some of the command-language enhancements which go beyond RasMol. Combine the powerful select menu, the copy script capability, and the ability to load any PDB file from your local hard disk (demonstrated at http://www.umass.edu/microbio/chime/chimehow/fs_cmdl2.htm -- view this with Navigator 4.01; 4.04 will give you 'too many' harmless but annoying javascript errors), and we have the tools for building powerful presentation development interfaces. No longer does one need the cumbersome dummy frame and 'immediate button' mechanism to send commands to Chime. A single line LiveConnect javascript function now does the trick (demonstrated as 'Javascript to Chime' at MDL's demo site). New button types supported in the text surrounding the image: toggle buttons which stay depressed when on, and radio buttons. Mind-blowing enhancements to Chime 2's infrastructure now support: Clickable spectra: click on a peak and see the bonds responsible highlighted. This was done in collaboration with Robert J. Lancashire (U West Indies, Jamaica). In conjunction with a free module from Sculpt, pull on an atom and watch real-time energy minimization modeling. Display molecular surfaces with built-in calculations for electrostatic potential or molecular lipophilicity potential color schemes. Excellent animation control -- watch the animation of a chemical reaction at the demo site. Not only all the above and more, but we now have DOCUMENTATION (at MDL's site)! Hooray for MDL! (pardon my enthusiasm) Hooray for Tim Maffett who is responsible for many of these enhancements, and who, I greatly regret, is currently recuperating from injuries suffered recently while snowboarding. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Lee Subject: simple problem Date: Mon, 05 Jan 1998 12:00:08 -0500 To: "rasmol@lists.umass.edu" Happy New Years to Everyone The problem is when I try to display ribbons in very large proteins such as 1mmo.pdb. If I write a script for the ribbon display, it will then take a long time to read this script because of the size of the file. I by-pass this problem by trying to type "select all" followed by "ribbon" in the actual script. The only problem with this is that it seems to superimpose the ribbon display onto the wireframe display. If this problem is not clear, load 1mmo.pdb then type "ribbon" and you will see what I mean. Thank you to anyone who replies. Sincerely Adrian Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: "Knapp, Dr. Darin" Subject: Re: simple problem Date: Mon, 5 Jan 1998 13:42:02 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu I am trying to unscubscribe to the rasmol list. No luck working with the automatied service. Anyone able to help me? Thanks. D. Knapp Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: "Knapp, Dr. Darin" Subject: Date: Mon, 5 Jan 1998 13:57:41 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Rasmolers, I am trying to unscubscribe to the rasmol list. No luck working with the automated service. Anyone able to help me? Thanks. D. Knapp ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: simple problem Date: Mon, 05 Jan 1998 14:51:17 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Just insert the command 'wireframe off' in your script to get rid of it. At 12:00 PM 1/5/98 -0500, you wrote: >Happy New Years to Everyone > > The problem is when I try to display ribbons in very large proteins >such as 1mmo.pdb. If I write a script for the ribbon display, it will >then take a long time to read this script because of the size of the >file. I by-pass this problem by trying to type "select all" followed by >"ribbon" in the actual script. The only problem with this is that it >seems to superimpose the ribbon display onto the wireframe display. If >this problem is not clear, load 1mmo.pdb then type "ribbon" and you will >see what I mean. Thank you to anyone who replies. > >Sincerely >Adrian > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: New PDB Mirror Sites Date: Thu, 08 Jan 1998 15:12:19 -0500 To: rasmol@dhcp-srv2.oit.umass.edu This message was sent to the RasMol list on Dec 23 but didn't get broadcast till now because of a technical failure. -Eric Martz ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Date: Tue, 23 Dec 1997 The PDB is very pleased to announce the availability of two new Official Mirror sites now on-line. These new sites will help to better serve the needs of users around the world by maintaining up-to-date copies of the PDB archives for access via the World Wide Web. These new mirrors have been established at: http://pdb.gmd.de/ The German National Research Center for Information Technology (GMD), Sankt Augustin, Germany http://pdb.icm.edu.pl/ The Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), Warsaw University, Poland These are now available from the PDB WWW Mirror Sites page, http://www.pdb.bnl.gov/pdb-docs/mirror_sites.html. On behalf of the PDB, I would like to welcome them and thank them for offering this service. There is now a total of 11 available PDB Mirror Sites: Cambridge Crystallographic Data Centre, UK EMBL Outstation, European Bioinformatics Institute, UK German National Research Center for Information Technology, Germany Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Brazil Interdisciplinary Centre for Modelling, Poland Institute of Physical Chemistry, Peking University, China National Tsing Hua University, Taiwan University of Georgia, USA University of San Luis, Argentina The Walter and Eliza Hall Institute of Medical Research, Australia Weizmann Institute of Science, Israel We thank all of our Mirrors for their efforts in maintaining these as up-to-date copies of the PDB Web and FTP servers. -- _______________________________________________________________________ Nancy Oeder Manning Protein Data Bank Head User Support Brookhaven National Laboratory oeder@bnl.gov Biology Department, Bldg. 463 (516) 344-5744 phone P.O. Box 5000 (516) 344-5751 FAX Upton, NY 11973-5000 USA _______________________________________________________________________ /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Three cheers Date: Sun, 11 Jan 1998 19:40:51 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I sent this message on Jan 4 but it didn't get into the history file (I have no idea why) and may not have been broadcast properly and so I'm resending it: In my previous message (Jan 3, "Chime 2 beta 2 is IMPRESSIVE!"), I said "Hooray for MDL". To place credit where credit is due, I'd like to put in a word of appreciation for Bryan van Vliet, head of the Chemscape & Chime development team at MDL. Bryan has held Chime development and the team together and on course during a very trying year, through illnesses, departures of staff, and other crises. So ... Three Cheers for Bryan!! (Hope I didn't embarass you Bryan, but it needed to be said!) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-ZSender: rowland.geoff@zetnet.co.uk ++++------+------+------+------+------+------+------+------+------+------+ From: Geoffrey Rowland Subject: Unit Cells and Axes Date: Thu, 15 Jan 1998 01:59:54 GMT To: rasmol@dhcp-srv2.oit.umass.edu Cc: rwland.geoff@zetnet.co.uk Hello All, Inspired by the RasMol home page and the many other sites around the web, I'm starting to use RasMol/Chime to develop some materials for A-level (pre-University) Science students. At the moment I am generating .pdb format files for some inorganic structures (elements, hydrides, oxides and chlorides). This has largely involved using Babel to convert files from CSSR (.xr) to .pdb format. Since it would be nice to show the unit cell for some or all of these files, I have also text-edited the CRYST1 line into the .pdb files. CSSR files contain the relevant crystallographic information but Babel does not convert this. However, if my understanding is correct, I have encountered a slight problem with the 'set axes on' and 'set unitcell on' commands in RasMol 2.6b (and hence also Chime?). If the Cartesian axes are displayed using 'set axes on' the Y-axis seems to be labelled in the negative direction rather than the positive direction. Similarly, at least when the unit cell has cubic symmetry (e.g. NaCl), the unit cell also seems to be drawn with the b axis pointing in the negative direction. Hence, if the x, y and z atom co-ordinates of a pdb file are all positive in value, the unit cell is drawn alongside, rather than enclosing, the atom positions. I would be most grateful if anyone could confirm if there is a problem and, assuming there is, suggest any work-around or fix - particularly if this does not involve recalculating the positions of all the atoms in all the files. Just sticking a minus sign in front of the b value of the CRYST1 record seems to work for cubic unit cells but I suspect this won't necessarily work for other symmetries. My 3-D geometry isn't up to this at the moment! In scanning previous Rasmol Emails I came across the following contribution by Hidehero Uekusa which seems to concern the same problem. >From: Hidehiro UEKUSA >Subject: Re: displaying crystals >Date: Tue, 04 Feb 1997 11:49:21 +0900 >To: rasmol@noc1.oit.umass.edu >In my experience in ver. 2.6, angles alpha and beta angle in 'CRYST1' >line should be 'inverted', i.e., subtracted from 180 degree when >composing 'CRYST1' line (if beta is 100 degree, enter 80 in the line. >But this might be my misunderstanding). Another problem, which may or may not be related to the above, is that if the line of a unit cell intersects an atom sphere the correct perspective (i.e. whether the line is partially hidden) is not always displayed. There seems to be a particular problem if there is an atom at the corners of the unit cell. Any ideas ? Many thanks, Geoff Rowland, Yeovil College Content-MD5: vfDO/FbLU7MdyAkQ4wtC+A== ++++------+------+------+------+------+------+------+------+------+------+ From: Erik Lindahl Subject: remove Date: Thu, 15 Jan 1998 08:19:58 +0100 (MET) To: rasmol@dhcp-srv2.oit.umass.edu > Date: Thu, 15 Jan 1998 01:59:54 GMT > From: Geoffrey Rowland > To: rasmol@dhcp-srv2.oit.umass.edu > Cc: rwland.geoff@zetnet.co.uk > Subject: Unit Cells and Axes > X-ZSender: rowland.geoff@zetnet.co.uk > X-Listprocessor-Version: 8.1 -- ListProcessor(tm) by CREN > > Hello All, > > Inspired by the RasMol home page and the many other sites around the > web, I'm starting to use RasMol/Chime to develop some materials for > A-level (pre-University) Science students. At the moment I am > generating .pdb format files for some inorganic structures (elements, > hydrides, oxides and chlorides). This has largely involved using > Babel to convert files from CSSR (.xr) to .pdb format. Since it would > be nice to show the unit cell for some or all of these files, I have > also text-edited the CRYST1 line into the .pdb files. CSSR files > contain the relevant crystallographic information but Babel does not > convert this. > > However, if my understanding is correct, I have encountered a slight > problem with the 'set axes on' and 'set unitcell on' commands in > RasMol 2.6b (and hence also Chime?). If the Cartesian axes are > displayed using 'set axes on' the Y-axis seems to be labelled in the > negative direction rather than the positive direction. Similarly, at > least when the unit cell has cubic symmetry (e.g. NaCl), the unit > cell also seems to be drawn with the b axis pointing in the negative > direction. Hence, if the x, y and z atom co-ordinates of a pdb file > are all positive in value, the unit cell is drawn alongside, rather > than enclosing, the atom positions. > > I would be most grateful if anyone could confirm if there is a > problem and, assuming there is, suggest any work-around or fix - > particularly if this does not involve recalculating the positions of > all the atoms in all the files. Just sticking a minus sign in front > of the b value of the CRYST1 record seems to work for cubic unit > cells but I suspect this won't necessarily work for other symmetries. > My 3-D geometry isn't up to this at the moment! > > In scanning previous Rasmol Emails I came across the following > contribution by Hidehero Uekusa which seems to concern the same problem. > > >From: Hidehiro UEKUSA > >Subject: Re: displaying crystals > >Date: Tue, 04 Feb 1997 11:49:21 +0900 > >To: rasmol@noc1.oit.umass.edu > > >In my experience in ver. 2.6, angles alpha and beta angle in 'CRYST1' > >line should be 'inverted', i.e., subtracted from 180 degree when > >composing 'CRYST1' line (if beta is 100 degree, enter 80 in the line. > >But this might be my misunderstanding). > > > Another problem, which may or may not be related to the above, is > that if the line of a unit cell intersects an atom sphere the correct > perspective (i.e. whether the line is partially hidden) is not always > displayed. There seems to be a particular problem if there is an atom > at the corners of the unit cell. > > Any ideas ? > > Many thanks, > > Geoff Rowland, Yeovil College > > --------------------------------------------------------------------- Erik Lindahl, PhD Student erik@theophys.kth.se Theoretical Physics, Royal Institute of Technology, STOCKHOLM, SWEDEN Phone: +46 8 7907172 Fax: +46 8 104879 ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Unit Cells and Axes Date: Thu, 15 Jan 1998 08:25:10 -0800 To: rasmol@dhcp-srv2.oit.umass.edu I believe that these two problems have been fixed in the Chime 2.0 beta that is now available at www.mdli.com -tim At 05:59 PM 1/14/98 -0800, you wrote: >Hello All, > >Inspired by the RasMol home page and the many other sites around the >web, I'm starting to use RasMol/Chime to develop some materials for >A-level (pre-University) Science students. At the moment I am >generating .pdb format files for some inorganic structures (elements, >hydrides, oxides and chlorides). This has largely involved using >Babel to convert files from CSSR (.xr) to .pdb format. Since it would >be nice to show the unit cell for some or all of these files, I have >also text-edited the CRYST1 line into the .pdb files. CSSR files >contain the relevant crystallographic information but Babel does not >convert this. > >However, if my understanding is correct, I have encountered a slight >problem with the 'set axes on' and 'set unitcell on' commands in >RasMol 2.6b (and hence also Chime?). If the Cartesian axes are >displayed using 'set axes on' the Y-axis seems to be labelled in the >negative direction rather than the positive direction. Similarly, at >least when the unit cell has cubic symmetry (e.g. NaCl), the unit >cell also seems to be drawn with the b axis pointing in the negative >direction. Hence, if the x, y and z atom co-ordinates of a pdb file >are all positive in value, the unit cell is drawn alongside, rather >than enclosing, the atom positions. > >I would be most grateful if anyone could confirm if there is a >problem and, assuming there is, suggest any work-around or fix - >particularly if this does not involve recalculating the positions of >all the atoms in all the files. Just sticking a minus sign in front >of the b value of the CRYST1 record seems to work for cubic unit >cells but I suspect this won't necessarily work for other symmetries. >My 3-D geometry isn't up to this at the moment! > >In scanning previous Rasmol Emails I came across the following >contribution by Hidehero Uekusa which seems to concern the same problem. > >>From: Hidehiro UEKUSA >>Subject: Re: displaying crystals >>Date: Tue, 04 Feb 1997 11:49:21 +0900 >>To: rasmol@noc1.oit.umass.edu > >>In my experience in ver. 2.6, angles alpha and beta angle in 'CRYST1' >>line should be 'inverted', i.e., subtracted from 180 degree when >>composing 'CRYST1' line (if beta is 100 degree, enter 80 in the line. >>But this might be my misunderstanding). > > >Another problem, which may or may not be related to the above, is >that if the line of a unit cell intersects an atom sphere the correct >perspective (i.e. whether the line is partially hidden) is not always >displayed. There seems to be a particular problem if there is an atom >at the corners of the unit cell. > >Any ideas ? > >Many thanks, > >Geoff Rowland, Yeovil College > > > > X-ZSender: rowland.geoff@zetnet.co.uk ++++------+------+------+------+------+------+------+------+------+------+ From: Geoffrey Rowland Subject: Re: Unit Cells and Axes Date: Thu, 15 Jan 1998 22:36:22 GMT To: rasmol@dhcp-srv2.oit.umass.edu Dear Tim et al., There still appears to be a problem. In my hands, Rasmol 2.6b, Chime 1.0 and Chime 2.0 beta 2 (which I've just downloaded and installed for the second time) all behave in the same way. In case it sheds any light on the problem, or identifies a flaw in my thinking, try the following pdb format file with a single body-centered cubic unit cell of sodium atoms. HEADER TEST XYZ/UNITCELL COMPND SODIUM BODY-CENTERED CUBIC UNIT CELL CRYST1 4.235 4.235 4.235 90.00 90.00 90.00 I M-3 M ATOM 1 Na UNK 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 Na UNK 1 2.118 2.118 2.118 1.00 0.00 ATOM 3 Na UNK 1 0.000 0.000 4.235 1.00 0.00 ATOM 4 Na UNK 1 0.000 4.235 0.000 1.00 0.00 ATOM 5 Na UNK 1 0.000 4.235 4.235 1.00 0.00 ATOM 6 Na UNK 1 4.235 0.000 0.000 1.00 0.00 ATOM 7 Na UNK 1 4.235 0.000 4.235 1.00 0.00 ATOM 8 Na UNK 1 4.235 4.235 0.000 1.00 0.00 ATOM 9 Na UNK 1 4.235 4.235 4.235 1.00 0.00 MASTER 0 0 0 0 0 0 0 0 9 0 9 0 END I would expect the 'set unitcell on' command or script to draw a unit cell starting from Na 1 (0,0,0) at the origin and linking the other 7 Na atoms at the corners. Indeed, this is what happens if you load the file into WebLab Viewer Pro and use the 'Tools, 'Crystal Cell' options. However Rasmol and Chime draw the unit cell in an immediately adjacent position. If you also use the 'set axes on' command/script you can see that the Y-axis points in the negative direction (towards the unit cell as drawn). If you rotate the structure there also appear to be some odd perspective effects where the unit cell intersects the atoms at the corners - in ball and stick mode. I eagerly await Chime 2.0 beta 3, or a brain-transplant, as appropriate :-) Geoff Rowland, Yeovil College > The message <3.0.32.19980115082503.00a2dc88@mind.net> from Tim Maffett contains these words: > I believe that these two problems have been fixed in the > Chime 2.0 beta that is now available at www.mdli.com > -tim > At 05:59 PM 1/14/98 -0800, you wrote: > >Hello All, > > > >Inspired by the RasMol home page and the many other sites around the > >web, I'm starting to use RasMol/Chime to develop some materials for > >A-level (pre-University) Science students. At the moment I am > >generating .pdb format files for some inorganic structures (elements, > >hydrides, oxides and chlorides). This has largely involved using > >Babel to convert files from CSSR (.xr) to .pdb format. Since it would > >be nice to show the unit cell for some or all of these files, I have > >also text-edited the CRYST1 line into the .pdb files. CSSR files > >contain the relevant crystallographic information but Babel does not > >convert this. > > > >However, if my understanding is correct, I have encountered a slight > >problem with the 'set axes on' and 'set unitcell on' commands in > >RasMol 2.6b (and hence also Chime?). If the Cartesian axes are > >displayed using 'set axes on' the Y-axis seems to be labelled in the > >negative direction rather than the positive direction. Similarly, at > >least when the unit cell has cubic symmetry (e.g. NaCl), the unit > >cell also seems to be drawn with the b axis pointing in the negative > >direction. Hence, if the x, y and z atom co-ordinates of a pdb file > >are all positive in value, the unit cell is drawn alongside, rather > >than enclosing, the atom positions. > > > >I would be most grateful if anyone could confirm if there is a > >problem and, assuming there is, suggest any work-around or fix - > >particularly if this does not involve recalculating the positions of > >all the atoms in all the files. Just sticking a minus sign in front > >of the b value of the CRYST1 record seems to work for cubic unit > >cells but I suspect this won't necessarily work for other symmetries. > >My 3-D geometry isn't up to this at the moment! > > > >In scanning previous Rasmol Emails I came across the following > >contribution by Hidehero Uekusa which seems to concern the same problem. > > > >>From: Hidehiro UEKUSA > >>Subject: Re: displaying crystals > >>Date: Tue, 04 Feb 1997 11:49:21 +0900 > >>To: rasmol@noc1.oit.umass.edu > > > >>In my experience in ver. 2.6, angles alpha and beta angle in 'CRYST1' > >>line should be 'inverted', i.e., subtracted from 180 degree when > >>composing 'CRYST1' line (if beta is 100 degree, enter 80 in the line. > >>But this might be my misunderstanding). > > > > > >Another problem, which may or may not be related to the above, is > >that if the line of a unit cell intersects an atom sphere the correct > >perspective (i.e. whether the line is partially hidden) is not always > >displayed. There seems to be a particular problem if there is an atom > >at the corners of the unit cell. > > > >Any ideas ? > > > >Many thanks, > > > >Geoff Rowland, Yeovil College ++++------+------+------+------+------+------+------+------+------+------+ From: "Jason D. Kahn" Subject: Text paste into Windows version command window? Date: Mon, 19 Jan 1998 10:26:35 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Hello, I'm using rasmol for presentation of biochemistry course material. In the interests of simplicity and of running on old computers I've steered away from Chime so far. Also, I'd like the students to learn to manipulate structures as well as appreciate them, and rasmol scripts hide a lot of these nuts and bolts. So, the point, I provide text files of rasmol commands which the students can use to recreate useful views of biomolecules. On Mac and Unix systems, the text can be copied/pasted or X-pasted from Netscape into the command window and everything works. However, under Windows 3.11 rasmol won't accept the paste. The method of saving the file as a script and then playing it back again tends to hide how the program works and prevents easy stepping through the script. Is there any way to paste text into the command window of the Windows version? Jason Kahn *- Jason D. Kahn Department of Chemistry and Biochemistry -* *- (301) 405-0058 University of Maryland -* *- fax 405-9376 College Park, MD 20742-2021 -* *- kahn@adnadn.umd.edu, http://www-chem.umd.edu/biochem/kahn/ -* References: <34C370AB.41C6@adnadn.umd.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Augusto Schuh Subject: Re: Text paste into Windows version command window? Date: Mon, 19 Jan 1998 14:06:40 -0300 (EST) To: rasmol@dhcp-srv2.oit.umass.edu I didn't tried, because I only use Rasmol for artwork. But I think in Windows 95 it will work. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime vs. Navigator 4.04 Date: Sat, 24 Jan 1998 17:53:27 -0500 To: rasmol@dhcp-srv2.oit.umass.edu On January 1, I described the solution to why many of my Chime resources (at http://www.umass.edu/microbio/chime/) failed under Navigator 4.04 despite working under Navigator 4.01. I have now upgraded my resources; I believe nearly all will now work with Navigator 4.04 and Chime 2 beta 3. The only exception (noted at http://www.umass.edu/microbio/chime/prereqs.htm) is my protein secondary sructure tutorial. I am planning to port this to the format used in my other recent tutorials (e.g. hemoglobin and antibody) and so am not upgrading it. It still works with Navigator 3.01 and Chime 1.0. The new versions are available for download, as always. Thanks again to Bryan van Vliet for tracking down the solution. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: 2 long-time Chime/Rasmol frustrations. Date: Sun, 25 Jan 98 16:31:28 -0800 To: "Rasmol Email List" Hello, I'm sharing a couple of things that have frustrated me for awhile in my work with Chime and Rasmol, in the hopes that some of you have found work-arounds for them. In the event that it is significant here (as far as different versions of Chime and Rasmol go), I am using a Power Mac 8500/233, Netscape 3.0x/Chime 1.0, and Rasmol 2.6. 1. Problems using GZipped files Anyone else find this annoying? In order for Chime to recognize a Gzipped .pdb file (for example), it must be renamed from filename.pdb.gz to filename.pdb. This is confusing for ftp clients, because it is now a binary file, but with an extension that suggests it is a text file (.pdb). So if my file-mapping is set to download a .pdb file as text (and type it as a Rasmol file), a binary GZipped .pdb will get corrupted if downloaded/uploaded. That is, unless I up/download the GZipped files separately and specify that they are binary. If you're up/downloading an entire site or tutorial at a time this is a hassle and easily forgotten if in a hurry. Then suprise, none of the models load, because they are all corrupt. Also, I've seen some strange issues where some Netscape/Chime on some Macs and PC's won't recognize Mac-created gzipped pdb files if their file type is left GZIP (default for MacGZip). If I change the file type to text they work. But then the custom icon that helps you tell the difference in directory listings between Gzipped and ordinary pdb files is lost. This is useful since Rasmol can't read GZipped pdb files and I frequently jumped between Rasmol and Chime when working on tutorials. It would be nice if Chime could recognize the .gz suffix in order to allow dedicated file-mapping for binary vs. text molecule files. Or has someone found a good work-around? 2. Chime cartoons vs. Rasmol cartoons; Blocky cartoons vs. smooth cartoons. OK, everyone must have noticed this. There are two different types of "cartoon" rendering. The ribbon and sheet structures themselves look about the same in both types. The difference is in the segments of non-helical or non-sheet residues. In Chime, if you select Display->Cartoons from the Chime menu, you get a nice, rounded-smooth rendering of these segments. If you tie a Rasmol script containing "cartoons true" to a button, you get a much blockier, square rendering. Similarly in Rasmol, if you use the command line "cartoons true" you get the blockier rendering. If you select Cartoons from the Display pulldown menu at the top of the screen, you get the smoother rendering. Is there any way to get the smoother cartoons rendering in Chime without forcing the user to use the Chime menu? I'd really like to use it in some of our tutorials, which generally use Rasmol scripts and (when it can't be avoided) JavaScript. thanks, Slaton Lipscomb C4: Computers in Chemistry at Cabrillo College http://c4.cabrillo.cc.ca.us/ ++++------+------+------+------+------+------+------+------+------+------+ From: Bryan Van Vliet Subject: Re: 2 long-time Chime/Rasmol frustrations. Date: Sun, 25 Jan 1998 22:57:47 -0500 To: rasmol@dhcp-srv2.oit.umass.edu >Anyone else find this annoying? In order for Chime to recognize a Gzipped >.pdb file (for example), it must be renamed from filename.pdb.gz to >filename.pdb. This is a function of your web server and not Chime. If you define the mime-type on your web server so that the file extension pdb.gz is mapped to chemical/x-pdb, then the file will be opened properly by Communicator, while Navigator 3.04 gives an alert, but then opens it anyway. Defining a mime type pdb_gz works for both Navigator and Communicator. I haven't tried Internet Explorer 4.0. You're a bit stuck on local files on your personal computer, but there's not much advantage to having the files compressed on your local hard drive (other than maintaining parity between your server and your desktop, of course.) In my humble opinion it would have been nice if Netscape and Microsoft and other companies writing web servers automatically handled compressed files and that we didn't have to do anything to offer this capability. After all, it seems like it would be useful to more than just a chemical/ biological structure plug-in. >Also, I've seen some strange issues where some Netscape/Chime on some >Macs and PC's won't recognize Mac-created gzipped pdb files if their file >type is left GZIP (default for MacGZip). If I change the file type to >text they work. Again, this is totally out of our control. Netscape instantiates our plug-in, and we are at their mercy. >OK, everyone must have noticed this. There are two different types of >"cartoon" rendering. The ribbon and sheet structures themselves look >about the same in both types. The difference is in the segments of >non-helical or non-sheet residues. I took a quick look through the code and didn't see anywhere that we were handling the two cases differently. Generally, our menu items quickly drop down into the script parser anyway, so you shouldn't see differences. The only thing I can think of is that you are forcing the palette when you go through the menu item and not when you are going through a script. You can get smoother output by selecting "Color" "Force Palette" or with the embed tag option palette=foreground. Note that this sometimes causes display anomalies in Navigator/Communicator, since they are very finicky about only picking from the 218 color palette they use. If I am missing something, send a test case to "chime-feedback@mdli.com" and we will look into it. - Bryan ---------------------------------------------------------------------- | Bryan Van Vliet bryan@mdli.com | | Director, Internet Technologies 510.895.1313 x1160 (Voice) | | MDL Information Systems, Inc. 510.352.2870 (Fax) | | 14600 Catalina Street, San Leandro, CA 94577 http://www.mdli.com | ---------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: Re: 2 long-time Chime/Rasmol frustrations. Date: Sun, 25 Jan 98 22:51:51 -0800 To: "Rasmol Email List" Thanks for the tips Bryan regarding configuring a server to map filename.pdb.gz to the chemical/x-pdb mime. Why didn't I think of that? You also said: >You're a bit stuck on local files on your personal computer, but there's >not much advantage to having the files compressed on your local hard drive >(other than maintaining parity between your server and your desktop, of >course.) However I used the same logic as above to configure my client-side browser to do the same thing. I just added the extension .pdb.gz to .pdb in the Netscape listing for chemical/x-pdb. It works fine for opening gzipped local files with the .pdb.gz extension. This is great. Of course for anyone to use one of our tutorials locally, they would have to configure their own Netscape similarly, but this is a big step in the right direction. Regarding my second question: >>OK, everyone must have noticed this. There are two different types of >>"cartoon" rendering. The ribbon and sheet structures themselves look >>about the same in both types. The difference is in the segments of >>non-helical or non-sheet residues. I may not have been clear enough in my question or perhaps this is a platform specific issue (I'm on a Mac). Attached to the end of this email is a letter I just sent to chime-feedback@mdli.com as you suggested, guiding a user through a specific example of what I'm describing. Sorry to everyone else about the length of this post. thanks, Slaton Lipsomb ------------------------- (Letter sent to chime-feedback@mdli.com 1/25/98) Hello, This is a follow-up to my post on Eric Martz's Rasmol Email List, regarding an irregularity between cartoon renderings in Chime (and Rasmol). Bryan Van Vliet suggested that I write in with a "test case". Here it is. It is easiest demonstrated in Rasmol, but the exact same problem exists in Chime. In case this is a platform-specific issue, I am using a Power Mac 8500/233, Chime 1.0, and Netscape 3.0x (NS 4 is still weird with Chime 1.0); also Rasmol 2.6. Do this: 1. Open a protein with Rasmol. Preferably a small one with some helices, sheets, and random structure. 2. Using the Colour pulldown menu, select Colour->Structure. 3. Using the Display pulldown menu, select Display->Cartoons. In this coloring scheme, usually alpha helices will be pink, beta sheets will be yellow, and random segments will be white (or blue, not sure how Rasmol/Chime decides). Zoom in so that you can clearly see a stretch of white random protein. Notice that it has a smooth, rounded appearance. Now: 1. Go to the command line and type "cartoons true". Notice that the rounded appearance of the non-helical/sheet protein has become blocky and squarish. The helices and sheets look the same, but the other segments look quite different. OK, this is what I was talking about referring to there being two different types of cartoon rendering in Chime and Rasmol. You get the smooth, rounder appearance in Chime if you use the Chime Menu to select Display->Cartoons, just like using the pulldown menu in Rasmol. You get the blocky square looking appearance if you use buttons tied to Rasmol scripts that use "cartoons true". I work on tutorials for instructor and student use that make extensive use of Chime. We do a lot of Rasmol scripting with buttons and Javascript to implement sequential rendering and movement changes in a given protein. Admittedly, it's partly an aesthetic issue - I like the look of the smooth cartoons better than the blocky ones - but it's also a matter of consistency. I'd like what the instructors or students select with the Chime menu to look the same as what we show them with Rasmol scripts and buttons. Is there a way to get the smoother-looking cartoons without using the Chime Menu? This is not a Netscape palette issue, since it happens in Rasmol as well as Chime. Using the embed option palette=foreground (as suggested) has no effect and does not appear to be involved. Many thanks, Slaton Lipscomb C4: Computers in Chemistry at Cabrillo College http://c4.cabrillo.cc.ca.us/ slaton@surfnetusa.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: 'Smooth' cartoons by command Date: Mon, 26 Jan 1998 18:06:53 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, chime-feedback@mdli.com, Slaton Lipsomb has recently called our attention to the differences in rendering achieved with Display->Cartoons (from the menu) vs. 'cartoons' from the command line (in both RasMol and Chime). I never noticed this before but I can see what he means. Here is my diagnosis and a proposed solution: The Display menu Cartoons is actually generating a hybrid rendering in which helices and sheets are rendered as solid ribbon cartoons (sheets with arrowheads), while turns and 'other' (blue and white in the secondary structure color scheme) are rendered as 'traces' (a smooth spline trace of the backbone alpha carbons). The 'cartoon' command renders everything in cartoon format: the helices and sheets are the same, but the turns and other are a square cylinder cartoon instead of a rounded cylindrical one. It appears to me that you can achieve the result of the menu with the following set of commands (which could be saved in a script file named cartoonm.spt [m for menu]). define temp selected select not (helix or sheet) trace 0.4 select temp Explanation: the first and last lines preserve whatever was the selected subset when cartoonm.spt was called. The 'select not ...' command selects the blue and white regions, and the trace command changes the rendering of these, leaving the helices and sheets as cartoons. By default, the 'trace' command seems to give a cylinder radius of 0.33 Angstroms, whereas the display menu cartoons uses about 0.4 Angstroms. A reminder concerning secondary structure may be in order. If helix, sheet, and turn records are present in the PDB file, RasMol/Chime obey them regarding the secondary structure colors, and the helix and sheet select commands. If the records are absent, RasMol makes its own determination (which usually differs slightly). If the records are present, you can force the application of RasMol's internal rules with the command 'structure'. When you first apply 'color structure' (from either the menu or the command line), if there is no report of the counts of helices, sheets, and turns, then records were present in the PDB file; if there is a report, the records were absent. The report is from the application of RasMol's internal rules. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: Re: 'Smooth' cartoons by command Date: Mon, 26 Jan 98 21:15:59 -0800 To: "Rasmol Email List" Eric Martz wrote: >The Display menu Cartoons is actually generating a hybrid rendering in >which helices and sheets are rendered as solid ribbon cartoons (sheets with >arrowheads), while turns and 'other' (blue and white in the secondary >structure color scheme) are rendered as 'traces' (a smooth spline trace of >the backbone alpha carbons). The 'cartoon' command renders everything in >cartoon format: the helices and sheets are the same, but the turns and >other are a square cylinder cartoon instead of a rounded cylindrical one. > >It appears to me that you can achieve the result of the menu with the >following set of commands (which could be saved in a script file named >cartoonm.spt [m for menu]). > >define temp selected >select not (helix or sheet) >trace 0.4 >select temp Excellent! Thank you Eric, this is exactly what I was looking for. I tried it out and it looks exactly the same. I wonder how it came to be in the first place that Rasmol's Display menu Cartoons uses this "hybrid rendering". It also makes me wonder if this is how Chime parses the Chime Menu Display->Cartoons command. >A reminder concerning secondary structure may be in order. If helix, >sheet, and turn records are present in the PDB file, RasMol/Chime obey them >regarding the secondary structure colors, and the helix and sheet select >commands. If the records are absent, RasMol makes its own determination >(which usually differs slightly). If the records are present, you can >force the application of RasMol's internal rules with the command >'structure'. When you first apply 'color structure' (from either the menu >or the command line), if there is no report of the counts of helices, >sheets, and turns, then records were present in the PDB file; if there is a >report, the records were absent. The report is from the application of >RasMol's internal rules. Thanks for the Rasmol lesson. Much appreciated. regards, Slaton Lipscomb C4: Computers in Chemistry at Cabrillo College http://c4.cabrillo.cc.ca.us/ ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: connect records - poof! Date: Thu, 29 Jan 1998 14:32:04 -0500 To: Rasmol I recently modified a structure within Rasmol, then saved it as a new pdb file using the Rasmol menu. When I opened the new pdb in a text editor, I noticed that all of the connect records were gone. I didn't notice anything different about the structure when I opened it in Rasmol again, though - I could zoom, rotate, ID atoms, etc. Has anyone else experienced this phenomenon? Could I be in trouble with more complex commands? Thanks, Tim ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: connect records - poof! Date: Thu, 29 Jan 1998 16:03:36 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I believe RasMol determines ALL bonds dynamically based on elements and distances, unless CONECT records are present for EVERY bond (rarely the case for macromolecule PDB files). The only exception I know about is that if there are CONECT records only for double bonds, it will obey these (see http://www.umass.edu/microbio/rasmol/faq_em.htm#doublebonds for a details and an example). N.B. that RasMol does not determine hydrogen bonds dynamically -- for these it uses simple (and sometimes wrong) rules for backbones and base pairs only. It cannot show Hbonds for nonbackbone, e.g. between proteins or sidechains. Both for saving subsets of atoms from PDB files and for dynamic Hbond determination, much better to use SwissPDBViewer than RasMol. It is also free and cross-platform. http://www.expasy.ch/spdbv/mainpage.htm Some of the differences in saving PDB files were documented recently at http://www.umass.edu/microbio/rasmol/pdbtools.htm, but I left out CONECT records. Nicolas Guex (author of SwissPDBViewer): does your program discard CONECT records? We probably need Roger Sayle to give us an authoritative rundown on whether RasMol ever saves CONECT records. It would be good to get this documented in the manual (which currently it is not). At 02:32 PM 1/29/98 -0500, you wrote: >I recently modified a structure within Rasmol, then saved it as a new >pdb file using the Rasmol menu. When I opened the new pdb in a text >editor, I noticed that all of the connect records were gone. I didn't >notice anything different about the structure when I opened it in Rasmol >again, though - I could zoom, rotate, ID atoms, etc. > >Has anyone else experienced this phenomenon? Could I be in trouble with >more complex commands? > >Thanks, > >Tim > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: reply to fax Date: Thu, 29 Jan 1998 17:26:03 -0500 To: drbob@uccaribe.edu (Dr. Robert Villafane ) Cc: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu At 11:33 PM 1/27/98 -0400, you wrote: > While I have your attention, a quick Rasmol >question, how do I determine what a hetero molecule is called in order to >do a restrict function on it? I work with the P22 phage tailspike protein >and it is an LPS-binding protein. There >available an x-ray structure of it in complex with its substrate LPS (1TYU, >1TYW, 1TYX, 1TSP). I can not tell which name to use for the LPS to do a >restrict. Would it be possible for you to tell me how to do it? Thanks. > with high hopes, Bob Robert Villafane Ph.D. >Assoc Prof of Microbiology >UCC Sch Med, Puerto Rico I took a look at 1tyu. The only thing other than protein and water is an octasaccharide. There are several ways to restrict to it. 1. 'restrict ligand' works fine. 'ligand' is defined as 'hetero and not solvent' by RasMol. (See the manual at http://www.umass.edu/microbio/rasmol/distrib/rasman.htm) 2. Examine the PDB file and note that the residues are designated GAL, MAN, TYV, RAM. 'restrict (gal or man or tyv or ram)'. Unfortunately RasMol has no predefined set term such as 'sugar' or 'carbohydrate'. (See the manual) 3. Inspect the PDB file and if the desired residues have a separate chain designation from the protein, such as chain S for sugar, 'select :s', but in this case there are NO chain designations in the PDB file. (You could use my NEWCHAIN.EXE program to add them but it would require cutting and pasting different parts of the PDB to get different chain letters, as my program is rudimentary and puts a single chain letter onto all ATOM records in the file it is given.) My program is at http://www.umass.edu/microbio/rasmol/pdbtools.htm#martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: gilkes@unixg.ubc.ca (Neil Gilkes) Subject: chime templates Date: Thu, 29 Jan 1998 14:51:58 -0800 To: rasmol@dhcp-srv2.oit.umass.edu I am having trouble using the U. Mass.chime template (Gal4 transcriptional regulator). When I open twoframe.htm in the Netscape browser (either Netscape v.3 or v.4), the left frame displays a broken plug-in icon. When I pass over the frame with the cursor I get the following message at the bottom of the window: cgi.netscape.com/eng/mozilla/2.0/extensions/plugin.cgi?application/x-unknown -content-type The same thing happens when I load 2FRMCONT.HTM from the chime antibody template folder. The U. Mass. antibody presentation works fine when accessed over the Web. Does anyone have any suggestions. Thanks. Neil R. Gilkes Department of Microbiology and Immunology University of British Columbia 6174 University Boulevard Vancouver, B.C., CANADA V6T 1Z3 Tel: (604) 822 6845 Fax: (604) 822 6041 ++++------+------+------+------+------+------+------+------+------+------+ From: "Naomi S. Boxall" Subject: A-DNA Date: Tue, 3 Feb 1998 10:19:14 +1300 To: rasmol@dhcp-srv2.oit.umass.edu Hi Does anyone know where I would be likely to find a pdb file on A-DNA? If not a pdb file, what could I use instead? Thanks in advance... ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Hubbard Subject: Re: A-DNA Date: Mon, 2 Feb 1998 22:13:35 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Dear Naomi, >Does anyone know where I would be likely to find a pdb file on A-DNA? If >not a pdb file, what could I use instead? Structures of A-form DNA in PDB are incidentally (though incompletely) classified in scop (structural classification of proteins database) although its main job is protein classification not DNA. It can be found at: http://scop.mrc-lmb.cam.ac.uk/scop/ and at mirrors around the world. Tim Hubbard ---------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Head, Human Genome Analysis Tel (direct): +44 1223 494983 Sanger Centre Tel (switch): +44 1223 834244 Wellcome Trust Genome Campus, Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. UK. URL: http://www.sanger.ac.uk/Users/th ---------------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Don Harden" Subject: Re: A-DNA Date: Mon, 2 Feb 1998 17:20:14 -0500 (EST) To: rasmol@dhcp-srv2.oit.umass.edu Naomi, You (and anyone else) are welcome to use any graphics or PDB files on our "PDB FILES FOR TEACHING BIOCHEMISTRY" web site: http://heme.Gsu.EDU/glactone/PDB/pdb.html The A-DNA is in the Nucleic Acids section. It is a theoretical model. If you want a PDB of a "real" A-DNA your best bet is the Nucleic Acid Database Project at Rutgers University (http://ndbserver.rutgers.edu), [assuming the PDB (http://www.pdb.bnl.gov/) doesn't have what you want] If you are looking for PDBs at the undergraduate biochem level, we have many proteins (at http://heme.Gsu.EDU/glactone/PDB/pdb.html) divided into the following categories: Classic Proteins: 12 classical proteins often studied in Biochemistry Nucleic Acid Binding Proteins: Eight common nucleic acid binding proteins Krebs Cycle: most of the enzymes involved in the citric acid cycle Gluconeogenesis and Glycolysis: most of the enzymes involved in gluconeogenesis and glycolysis Photosynthesis: many of enzymes the involved in photosynthesis Good hunting, Don On Tue, 3 Feb 1998, Naomi S. Boxall wrote: > Date: Tue, 3 Feb 1998 10:19:14 +1300 > From: "Naomi S. Boxall" > Reply-To: rasmol@lists.umass.edu > To: rasmol@dhcp-srv2.oit.umass.edu > Subject: A-DNA > > Hi > > Does anyone know where I would be likely to find a pdb file on A-DNA? If > not a pdb file, what could I use instead? > > Thanks in advance... > > > ---------------------------------------------------- Dr. Don Harden don-harden@Gsu.EDU Department of Chemistry Georgia State University ph: (404) 651-3580 Atlanta, Ga. 30303 fax: (404) 651-1416 http://heme.Gsu.EDU/glactone X-pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Phyllis Dewar" Subject: Re: A-DNA Date: Mon, 2 Feb 1998 20:14:47 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Naomi, A-DNA, B-DNA and Z-DNA an be found at http://heme.Gsu.EDU/glactone/PDB/DNA_RNA/dna.html Phyllis > Date: Tue, 3 Feb 1998 10:19:14 +1300 > Reply-to: rasmol@lists.umass.edu > From: "Naomi S. Boxall" > To: rasmol@dhcp-srv2.oit.umass.edu > Subject: A-DNA > Hi > > Does anyone know where I would be likely to find a pdb file on A-DNA? If > not a pdb file, what could I use instead? > > Thanks in advance... > > > Phyllis D. Dewar Department of Science Chowan College Murfreesboro, NC 27855 Voice: 919.398.6217 FAX: 919.398.1362 ++++------+------+------+------+------+------+------+------+------+------+ From: "J.Lin" Subject: How to save rotated coordinates? Date: Thu, 5 Feb 1998 11:21:30 +0100 (MET) To: rasmol@dhcp-srv2.oit.umass.edu Dear all, In fact, I have two questions. The first one is: when I rotate one molecule with RasMol, I want to save the current coordinates into a new PDB file, so that next time when I load this new PDB file, I can see the orientation I want. It would be also very nice if I can also set the center of the screen as the origin of my new PDB file. If these can be achieved, then I could combine several PDB files into one file. Can anybody give me some hints? The second questions is: in viewing the structure of a protein or peptide, it would be very nice to see the relation between the backbone and the side chains. I wonder if it's possible to see backbone and side chains ( maybe presented by big balls ) simultaneously by RasMol. Any reply is gratefully acknowledged! Best regards, Jung-hsin Lin -- -------------------------------------------------------------------------------- Jung-hsing Lin Forum Modellierung und Institut fuer Festkoerperforschung Forschungszentrum Juelich GmbH. D-52425 Juelich. Germany Phone (Office): +49-2461-61-2515; Fax: - 2983; email: j.lin@fz-juelich.de Phone/Fax (Home): +49-2461-54419; Addr: Muenchener Str. 5, D-52428 Juelich, Germany ------------------------------------------------------------------------------ References: <05180036002142@surfnetusa.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: How to save rotated coordinates? Date: Thu, 05 Feb 1998 12:16:21 -0500 To: J.Lin@fz-juelich.de Cc: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu At 11:21 AM 2/5/98 +0100, you wrote: >In fact, I have two questions. The first one is: when >I rotate one molecule with RasMol, I want to save >the current coordinates into a new PDB file, so that >next time when I load this new PDB file, I can see >the orientation I want. It would be also very nice >if I can also set the center of the screen as the >origin of my new PDB file. If these can be achieved, >then I could combine several PDB files into one file. >Can anybody give me some hints? Neither RasMol nor Chime can save rotated coordinates or centers, but SwissPDBViewer (also free, also Mac or Windows) can. Details are at http://www.umass.edu/microbio/rasmol/pdbtools.htm >The second questions is: in viewing the structure of >a protein or peptide, it would be very nice to see >the relation between the backbone and the side chains. >I wonder if it's possible to see backbone and side >chains ( maybe presented by big balls ) simultaneously >by RasMol. > >Jung-hsin Lin >Forum Modellierung und Institut fuer Festkoerperforschung >Forschungszentrum Juelich GmbH. D-52425 Juelich. Germany When you select a rendering (backbone or ball-and-stick for example) from the Display MENU, other renderings for the selected atoms are turned off. In contrast, when you apply renderings from the command line, other renderings remain on. So, for example, with all atoms selected, you can show both the backbone and the sidechains with: backbone 0.5 # The next two commands are equivalent to the Display Menu's # 'Ball and stick' rendering. wireframe 0.15 spacefill 0.48 There are predefined sets which can be used to 'select backbone' (alpha carbons) or 'select sidechain' if you wish, before applying renderings. You suggest that sidechains might be displayed as 'big balls'. I'm not sure what is the best way to do this and perhaps others can make suggestions. Here is what first comes to mind. You can select all the beta carbons and spacefill them as big as you want. For example, backbone 0.5 select *.cb spacefill 1.5 This would show all sidechains except glycine. Since X-ray diffraction crystal-derived PDB's lack hydrogens (unless they have been modeled in), you won't usually be able to display those. Have fun, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: multimedia projector Date: Thu, 5 Feb 1998 12:31:16 -0500 To: rasmol@dhcp-srv2.oit.umass.edu List Members, We are looking for a good quality, high resolution computer-screen projection system. Preferably one that can connect to Macs, PCs, and SGIs, and be fairly portable. Can anyone point me to a good system? Thank you very much. Regards, Nancy -- _______________________________________________________________________ Nancy Oeder Manning Protein Data Bank Head User Support Brookhaven National Laboratory oeder@bnl.gov Biology Department, Bldg. 463 (516) 344-5744 phone P.O. Box 5000 (516) 344-5751 FAX Upton, NY 11973-5000 USA _______________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: "J.Lin" Subject: Re: How to save rotated coordinates? Date: Thu, 5 Feb 1998 19:31:39 +0100 (MET) To: rasmol@dhcp-srv2.oit.umass.edu Dear Eric, Thank you very much for your detailed reply. > > >if I can also set the center of the screen as the > >origin of my new PDB file. If these can be achieved, > >then I could combine several PDB files into one file. > >Can anybody give me some hints? > > Neither RasMol nor Chime can save rotated coordinates or centers, but > SwissPDBViewer (also free, also Mac or Windows) can. Details are at > > http://www.umass.edu/microbio/rasmol/pdbtools.htm > It's really a pity that SwissPDBViewer is only implemented on Mac or PC, whereas I use a DEC alpha. It seems that I have to manipulate these coordinates by, say, awk. Best regards, Jung-hsin -- -------------------------------------------------------------------------------- Jung-hsing Lin Forum Modellierung und Institut fuer Festkoerperforschung Forschungszentrum Juelich GmbH. D-52425 Juelich. Germany Phone (Office): +49-2461-61-2515; Fax: - 2983; email: j.lin@fz-juelich.de Phone/Fax (Home): +49-2461-54419; Addr: Muenchener Str. 5, D-52428 Juelich, Germany ------------------------------------------------------------------------------ References: <9802051831.AA26206@iff002> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: How to save rotated coordinates? Date: Thu, 05 Feb 1998 22:39:21 +0100 To: J.Lin@fz-juelich.de Cc: rasmol@dhcp-srv2.oit.umass.edu J.Lin wrote: > > It's really a pity that SwissPDBViewer is only implemented on Mac or > PC, whereas I use a DEC alpha. It seems that I have to manipulate > these coordinates by, say, awk. What OS are you running?? UNIX (DEC/OSF ??) or NT? If you are using NT, there is an excellent emulator from DEC (called fx32!) which should enable your system to run Intel 32bit-code. I should also draw your attention towards Molmol, a free molecular modelling program developed at ETH Zürich. It might be able to do what you want. And it is available for almost every system running UNIX and NT/Win95 (no Mac). In case that it does not work for the DEC, you can download the sources and recompile it by yourself. For more information see http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/ -----BEGIN PGP SIGNATURE----- Version: PGP for Personal Privacy 5.0 Charset: noconv iQA/AwUBNMp1DRQHQPcpGdKHEQJJKQCg7rXNo2cf2KAxX4G1Dx5JoEIZNpkAn1zH vlnrohT9/RjfjlyjfNa7prUD =C/ql -----END PGP SIGNATURE----- ++++------+------+------+------+------+------+------+------+------+------+ From: Scot Wherland Subject: Chime/Helpers Date: Thu, 5 Feb 1998 16:46:08 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu I have set up a web page (http://www.wsu.edu/~wherland/)with a collection of molecules taken from crystal structures. The purpose is for students to be able to view and measure experimental structures and compare the parameters to those predicted by tables of radii, shape predictions models, etc. I also use Chime for another feature of the page (a periodic table of radii). In order to keep the two types of structure files distinct I used the WebLab viewer and their file format (msv) for the crystal structure data and stayed with pdb for the Chime files. On the PC this worked. However, Mac users do not have the option of using WebLab viewer, and the UCB extension to RasMol allows measurement of structures, so this seemed like an answer. I converted about 200 files to to a format readable by RasMol(UCB) (MDL mol files). That is the end of what worked. Without changing anything, these mol files will come up in Chime (1.0) for viewing. In order to measure them I need to force mol files to be viewed with RasMol(UCB) as a helper. On the Mac using Netscape 4.04 this is apparently possible (Edit/preferences/navigator/applications...), but although the helper (RasMol) comes up, it does not show the file. Trying to manually load the file that was downloaded also fails (only Chime shows it). On the PC I cannot edit the preferences to change to a helper for mol files, but on the PC I do not really need it. Any help is appreciated. Scot Scot Wherland Voice: 509-335-3360 Prof. of Chemistry FAX: 509-335-8867 Dept. of Chemistry Email: scot_wherland@wsu.edu Washington State University Pullman, WA 99164-4630 USA ++++------+------+------+------+------+------+------+------+------+------+ From: Andy Bates Subject: Re: multimedia projector Date: Fri, 6 Feb 1998 09:16:25 +0000 To: rasmol@dhcp-srv2.oit.umass.edu >List Members, > >We are looking for a good quality, high resolution computer-screen projection >system. Preferably one that can connect to Macs, PCs, and SGIs, and be fairly >portable. Can anyone point me to a good system? > >Thank you very much. > Nancy and everyone, We have an InFocus LitePro 720, which we like a lot. It's relatively light (about 12 lb), and hence fairly portable, even in a hard case, it's bright - pretty well as good as a regular slide projector, and the connections to Macs and PCs are very easy, since it has a neat cabling system which revels either Mac or PC connections by rotating a ring (inevitably, it's called a Cable Wizard :-). I have never connected to an SGI machine, but since the projector can take just about any kind of video input (and adjust itself to the relevant resolution more or less automatically), then I'm sure it should be no problem. The LCD screen at the heart of it has 800x600 pixels; you can of course project 640 x 480 as a smaller image, but other resolutions are accomodated by compression, which is ok, but not as clean as 1:1 correspondence between input and output resolution. I'm sure you can now get larger resolution machines these days (at a price) but 800X600 is good enough for our applications. If you want to project over a large distance, then you would need an optional long focus lens (The standard one zooms over a small range, so you can optimise the image size). It cost us (in the UK) around 7500 sterling, including the case, an extension to the cable system, and a couple of spare lamps. All in all, this had slightly less features than some others, but scored very highly on ease of use, which for us with multiple users was highly significant. It really is plug and play with a PC or Mac. Standard disclaimer - I have no connection with LitePro or their distributors... Cheers, Andy. __________________ Dr Andrew D. Bates School of Biological Sciences University of Liverpool Life Sciences Building Crown Steet Liverpool L69 7ZB UK Tel-(+44) (0)151 794 4322 Fax-(+44) (0)151 794 4349 Email-bates@liv.ac.uk http://www.liv.ac.uk/biolsci/html/gsrg_staff_0.html ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Re: Chime/Helpers Date: Fri, 6 Feb 1998 10:11:26 +0000 To: rasmol@dhcp-srv2.oit.umass.edu >I have set up a web page (http://www.wsu.edu/~wherland/)with a collection of >molecules taken from crystal structures. The purpose is for students to be >able to view and measure experimental structures and compare the parameters >to those predicted by tables of radii, shape predictions models, etc. I also >use Chime for another feature of the page (a periodic table of radii). In >order to keep the two types of structure files distinct I used the WebLab >viewer and their file format (msv) for the crystal structure data and stayed >with pdb for the Chime files. On the PC this worked. However, Mac users do >not have the option of using WebLab viewer, Why not? I have a copy of it (WebLab viewer) on my Mac? _____________________________________________________________________ Fergus Doherty PhD, Molecular and Cell Biology Section, D Floor, School of BioMedical Sciences, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH mailto:Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html Teaching URL: http://www.nottingham.ac.uk/~mbzmail/students/student.html "Re: multimedia projector" (Feb 6, 9:16am) References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Dawei Lin" Date: Fri, 6 Feb 1998 09:44:16 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu Dear Macromolecular Structure funs, Please see the note from Guy Riddihough. You can also find some discussion are going on the PDB listserver(http://www.pdb.bnl.gov). ---------------------------------------------------------------------- In light of the various ongoing discussions of the one year hold for structure coordinates, we are hosting a vote on the matter on the Nature Structural Biology web site, based on a petition to the IUCr proposed by Alex Wlodawer. I know that the journals Science and Nature, the IUCr, the PDB and the NIH are interested in the results we will obtain so potentially, the data may be of some importance in guiding discussions of future policy. For the vote to best represent the feelings in and beyond the structure community it is vital that as many people vote as possible. Thus I am e-mailing you to ask if you, and your colleagues, would be interested in contributing your opinions on the matter. The URL for the site of the vote is: http://us.nature.com/survey/nsb_poll.nclk I would not object if you wished to forward this message on to other colleagues, either structural biologists or scientists with an interest in the availability of structural data, whom you think may also want to express their opinion on the matter. If you have any questions regarding this or any other matter, please don't hesitate to contact me at this address or tel: 212 726 9313, fax: 212 679 0735. Sincerely Guy Riddihough Editor, Nature Structural Biology-- -- --------< *** Dr. Dawei LIN *** >--------------- Protein Data Bank Biology Department Brookhaven National Laboratory Upton, NY 11973 U.S.A Telepone: 516-344-6359 (office) Fax: 516-344-5751 Email: lin@bnl.gov ------------------------------------------------ ++++------+------+------+------+------+------+------+------+------+------+ From: Scot Wherland Subject: Re: Chime/Helpers Date: Fri, 6 Feb 1998 11:38:13 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Big oops! (and a lot of somewhat wasted effort). There certainly is a WebLab Viewer Lite (free) for the Mac and it works just fine. The full WebLab product is the one that is not currently available for the Mac. I will leave the mol files on the site for those who just want to look at the molecules quickly (Chime comes up quickly) and to provide ascii files. The other process still should have worked, and there are advantages to measuring the structures with RasMol(UCB)(as well as different advantages for WebLab), but I am happy to have it work for both communities. With some emabarassment, Scot Scot Wherland Voice: 509-335-3360 Prof. of Chemistry FAX: 509-335-8867 Dept. of Chemistry Email: scot_wherland@wsu.edu Washington State University Pullman, WA 99164-4630 USA ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: [Fwd: Still can't see graphics] Date: Mon, 09 Feb 1998 12:54:55 -0500 To: Rasmol LIST This is a multi-part message in MIME format. --------------83EECCC3F6105E7D5332CF2A Has anyone else encountered this problem running Chime on Netscape 3.0 on a Macintosh? --------------83EECCC3F6105E7D5332CF2A Content-Disposition: inline Resent-Date: Mon, 9 Feb 1998 12:24:44 -0500 (EST) Resent-From: Resent-to: tdriscol@unix.amherst.edu Resent-message-id: <01ITDJHNIC9G8XA55H@amherst.edu> X-VMS-To: IN%"tdriscoll@amherst.edu" "Timothy Driscoll" X-VMS-Cc: IN%"emartz@microbio.umass.edu" References: <34DE192F.5BBD@csulb.edu> <34DF348A.BF754239@amherst.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey A. Cohlberg" Subject: Still can't see graphics Date: Mon, 09 Feb 1998 09:22:22 -0700 To: Timothy Driscoll Cc: emartz@microbio.umass.edu Timothy Driscoll wrote: > > Jeff, > > There are other Chime tutorials on Protein Scondary Structure on the Web, > though they may not be as adaptable as Eric's protsecs. They can give an idea > of what is possible in Chime. > > For instance, check out http://www.amherst.edu/~connlab/biochem420. This is a > brief broad coverage of the topic, designed for a specific class lecture so > it's not as user-friendly as others may be (but it's the one that I remember > off the top of my head!). There are also a few minor problems that escaped > initial debugging. Beyond that, though, this is a good view of how you can do > simple yet powerful things with Chime. I can let you have the files for your > own use if you want; just let me know. > > Good luck! > > Tim I tried this web site, and once again the graphics didn't show up -- I got a blank square with the torn page icon in the center. The same thing happened when I tried to view the hemoglobin tutorial. I think I must be missing some plug-in. Is there a specific plug-in used to view the graphics in these files (other than the Chime plug-in), rather than just the normal Netscape software? Note: When I follow the link on the hemoglobin page "How to use Chime", I also get the torn page icons instead of the three graphics at the top of the page. I am a relatively frequent user of the Web, and this is not a universal problem for me -- there are lots of web pages where the graphics come in without a problem. Help!! Jeff -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840 phone (562) 985-4944 fax (562) 985-8557 --------------83EECCC3F6105E7D5332CF2A-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Naomi S. Boxall" Subject: Re: [Fwd: Still can't see graphics] Date: Tue, 10 Feb 1998 10:07:35 +1300 To: rasmol@dhcp-srv2.oit.umass.edu I'm running exactly the same programs on my macintosh and can see all the graphics clearly...perhaps something went wrong when you downloaded Chime? (I'm using Chime 1.0 - not the new version) Also...I have completed a section of tutorials on biochemistry, and would appreciate it if some of you could have a quick look at what is there and let me know your views. I am pretty sure they won't run too well on IE (having designed them for NN) but I would like to see/hear what they look like on the PC platform. The address is http://www.massey.ac.nz/~wwbioch/Prot/tutehome/tutepage.htm Thanks in advance... ____________________________________________________________ | Naomi S Boxall BSc Ph. 064-6-356-9099 ext.4058 | | Biochemistry Department Fax. 064-6-350-5688 | | Massey University e-mail. Naomi.Boxall.1@uni.massey.ac.nz | | Palmerston North | | New Zealand | -------------------------------------------------------------------------------- ---------------------------------------- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: [Fwd: Still can't see graphics] Date: Mon, 09 Feb 1998 18:15:03 -0500 To: rasmol@dhcp-srv2.oit.umass.edu The problem of the busted graphic icon was solved - make sure you leave Netscape in the same folder as the Plug-ins folder, or none of the Plug-ins will load (Mac). Thanks! ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Optimal format for Chime presentations Date: Tue, 17 Feb 1998 14:09:45 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu This message discusses pros and cons of various Chime presentation formats, and offers a ready-made template for a new one which combines several desirable features. NAVIGATION vs. LEGIBILITY The first format utilized for Chime presentations had a series of buttons interspersed in text in one frame, with the Chime graphic in a second frame. This format was pioneered by Tim Maffett, Henry Rzepa, and David Marcey to the best of my knowledge. One disadvantage of the earlier presentations was that the text was rather small, and hard to read when projected to a group. In part to deal with this limitation, I created a new format for linear presentations, illustrated by my presentation on protein secondary structure, ProtSecS, (http://www.umass.edu/microbio/chime/protsecs/index.htm). It has large text, including a large color key, in a frame at the bottom, and uses more of the screen for the Chime graphic. Having observed both formats being projected in large classes, I have concluded that the navigational control in my ProtSecS format is inadequate. It is too difficult to jump directly to any desired image, for example in response to a question, or when the lecturer wishes to show only a subset of the available images. So while the legend is more readable from the back of the room, the absence of the button-in-text map of the presentation (which easily allows hopping about randomly to any desired image) was too great a sacrifice. SYNTHESIS: NAVIGATION WITH LEGIBILITY Recently, in discussion with Tim Driscoll and Rashie Athukorala, we realized that variable font-size control could be implemented in the earlier format. I have now done this in the template I provide for building new presentations, version 2, (http://www.umass.edu/microbio/chime/prsswc/template.htm) and in our presentation on Hemoglobin (http://www.umass.edu/microbio/chime/hemoglob/index.htm). These two presentations follow the earlier format (allowing random jumping). Now you can choose a small font (making it easy to see a whole range of buttons and the overview of the present topic), or a large font visible at the rear of a large audience. Font size can be varied at any time, and remains in effect for all topics in the current session. Instructions are provided for retrofitting existing Chime presentations with this font control. The handful of necessary files can be downloaded as part of the 'minimal template fileset' needed to build a new presentation. TRUE RANDOM ACCESS: INDEPENDENT BUTTONS While the early format allowed pushing the buttons in any order, most such presentations on the web are not implemented so as to give the correct images when this is done. That is, the scripts attached to buttons are not independent; many scripts assume that the the previous button was pushed immediately previously. One easy way to make scripts which are independent is to save them from RasMol (or from Chime 2, which has fixed most of the few bugs in RasMol's script-saving mechanism). Such scripts always begin with a fresh start, loading the desired PDB file. Indeed, if all the scripts in a Chime presentation are saved from RasMol, one does not need to learn how to program RasMol/Chime script language. This is why in my NSF-supported workshops for faculty (http://www.umass.edu/microbio/rasmol/workshop.htm), we attach RasMol-saved scripts to buttons in a pre-existing Chime template. The template avoids needing to know HTML or javascript. This relatively easy method of creating a Chime presentation has the large advantage that all buttons are independent. Instructions for saving scripts and using the template, complete with troubleshooting, are available (http://www.umass.edu/microbio/chime/prsswc/template.htm), and the template can be downloaded. It may seem terribly inefficient to reload the PDB file for every button in a presentation, especially if a very large PDB file is used over and over. Luckily, IT IS NOT. First, after the PDB file (hopefully gzipped!) has been transmitted one time, all subsequent reads are done from the local cache. Second, Chime 2, by default, is intelligent enough to ignore a load command which specifies the same PDB file already loaded; it just resets everything as though a fresh load had occurred without actually reloading (thanks to Tim Maffett for implementing this!). I am interested to hear the insights and comments of others on these issues. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: PDB copyrights Date: Tue, 17 Feb 1998 15:00:30 -0500 To: "Owen Lofthus, II" Cc: rasmol@dhcp-srv2.oit.umass.edu At 2/17/98 , Owen W. Lofthus, II wrote: >Hello, > >I am a graduate student at Virginia Tech, and have been put in charge of >gathering information regarding chime and posting molecules on the web. >One question which I am unsure if is copyrighting. If I download a >molecule from a website, may I post it on mine? Or do I draw it, then post >it? I have already looked over some of your web pages and have learned >much about CHIME. If you could lend any advice, it would be greatly >appreciated. > >Thank you, > >Owen W. Lofthus, II >olofthus@vt.edu >http://www.vt.edu:10021/O/olofthus/index.html >Virginia Polytechnic Institute & State University >Blacksburg, VA 24061 It is my impression that PDB files (atomic coordinate files for molecules) which are published and publically available from the Brookhaven Protein Data Bank may be redistributed from another server (e.g. as part of a Chime presentation), provided the PDB file is suitably identified, and the authors of the PDB file(s) are suitably acknowledged in the presentation. I would appreciate comments from Nancy Oeder-Manning of BNL or others on this issue. It is also imperative that MODIFICATIONS to any PDB files be clearly stated as a remark at the top of the modified PDB file. I recently viewed a Chime presentation in which all sidechain atoms had been deleted from the PDB files, but this was not stated anywhere. This was very confusing. There should at least be a remark at the top of the PDB file stating what modifications were made to the original, and preferably the file should be renamed so as not to confuse it with the original, and of course there should be explicit mention of such modifications in the presentation text. If you download something from a private server, you must comply with the copyright restrictions stated there. It would also be best to ask explicit permission to redistribute any information obtained from a private server. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <0EOJ00L4NC266W@pobox1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Optimal format for Chime presentations Date: Tue, 17 Feb 1998 18:04:28 -0500 (EST) To: rasmol@dhcp-srv2.oit.umass.edu Eric, Two formats (and some new Chimed topics) that work here are: 1. Tutorial on tRNA, starting at: http://info.bio.cmu.edu/Courses/BiochemMols/tRNA_Tour/tRNA_Tour.html (This is a frames format with a selection menu covering several aspects of tRNA structure.) 2. Molecular Biology Structures, starting at: http://info.bio.cmu.edu/Courses/BiochemMols/MolBiol/MolBiol.html (This is a linked-page format that provides a one-page intro to seven molecules used in our Mol Biol courses. The second set of pages is converted easily to lecture presentation by increasing the Chime image to 500x500 from 350x350. Some minor HTML editing is involved, and two pages are required for each topic, but everything else is the same on both pages. -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: "Hidetoshi Kono(Jouhou)'950914" Subject: vectps Date: Wed, 18 Feb 1998 11:50:59 +0900 To: rasmol@dhcp-srv2.oit.umass.edu Cc: hkono@rtcmain.rtc.riken.go.jp Dear all, I have a question about vectps. Vectps creates a nice image, so, I would like to save a stereo image in the vectps format. But only left hand image are saved. Is it impossible to save a stereo image using vectps ? I am using rasmol2.6b2 under IRIS 6.2. Thanks in advace. Hidetoshi Kono --------- __o Tsukuba Life Science Center, RIKEN __________ -\<, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305 Japan ..... O/ O hkono@rtc.riken.go.jp Tel:81 298 36 9082 Fax:81 298 36 9080 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: vectps Date: Wed, 18 Feb 1998 13:50:08 -0500 To: rasmol@dhcp-srv2.oit.umass.edu The RasMol Manual http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual specifically states that stereo is one thing vectps does not support. Stereo was the last feature added to RasMol, and one of the reasons the current version is still a 'beta test' version is that stereo was never fully integrated with other aspects of the program. Also the manual was never officially updated (the above version is close to up to date, but not done by Roger Sayle), and the on-line help has not been updated since version 2.5. At 2/18/98 , you wrote: >Dear all, > >I have a question about vectps. >Vectps creates a nice image, >so, I would like to save a stereo image in the vectps format. >But only left hand image are saved. >Is it impossible to save a stereo image using vectps ? >I am using rasmol2.6b2 under IRIS 6.2. > >Thanks in advace. > >Hidetoshi Kono --------- __o >Tsukuba Life Science Center, RIKEN __________ -\<, >3-1-1 Koyadai, Tsukuba, Ibaraki, 305 Japan ..... O/ O >hkono@rtc.riken.go.jp Tel:81 298 36 9082 Fax:81 298 36 9080 > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Win32S: faster RasWin under Windows 3.1 Date: Wed, 18 Feb 1998 18:44:54 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Windows 3.1 users can double the speed of RasMol by using the 32-bit version of RasWin -- if they have a 386 or better with floating point hardware (e.g. 387), and if they install a free module called Win32SOle from Microsoft. On the RasMol Home Page, the link to Win32SOle has been broken for some time and several people have pointed this out. Unfortunately, Microsoft keeps changing the URL and breaking our link. Thanks to Rashie Athukorala, the link is fixed again. More info and the link is on our page at http://www.umass.edu/microbio/rasmol/getras.htm#raswin where you will also find instructions on how to install this module. and the link itself is ftp://ftp.microsoft.com/softlib/MSLFILES/PW1118.exe or http://support.microsoft.com/download/support/mslfiles/Pw1118.exe /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page (http://www.umass.edu/microbio/rasmol) - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: CPK, vectps now in manual Date: Thu, 19 Feb 1998 19:41:04 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: wm0p@andrew.cmu.edu, sears@lifesci.ucsb.edu I have updated the RasMol Manual http://www.umass.edu/microbio/rasmol/distrib/rasman.htm to include the complete and correct CPK color scheme as implemented in RasMol and Chime (taken directly from the source code of RasMol) in decimal (for RasMol or Chime) and hexadecimal (for Navigator) RGB values, and also a GIF image showing all 16 colors and the elements they map to. If you want to see the GIF image without the RGB data (and the rest of the 150K manual), go to http://www.umass.edu/microbio/rasmol/distrib/cpk.gif I have included some color patches to show colors difficult to distinguish. Notably, Zn and Li are only very slightly different; S, P, and F are similar variants of yellow. There is also a different GIF image of the CPK color scheme consisting of bars of color on a white background, suitable for printing ("RasMol's Flag"?). http://www.umass.edu/microbio/rasmol/distrib/cpk_barw.gif Also I noted that 'write vectps' was not mentioned in the manual, and added it. It is left as an exercise for the reader to guess why Roger Sayle assigned a unique color to helium. (If anyone solves this exercise, please share the solution!) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page (http://www.umass.edu/microbio/rasmol) - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: More font size control Date: Thu, 19 Feb 1998 20:39:26 -0500 To: rasmol@dhcp-srv2.oit.umass.edu The antibody and MHC Chime presentations at http://www.umass.edu/microbio/chime/ now have font size control. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page (http://www.umass.edu/microbio/rasmol) - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Baffled by Chime Date: Wed, 04 Mar 1998 14:10:15 -0500 To: debanzie Cc: rasmol@dhcp-srv2.oit.umass.edu At 3/3/98 , you wrote: >Dear Dr. Martz, > >... with anything [Chime] loaded off my hard drive (your page or a trial page I >wrote) I get a message saying that I need a plug-in to deal with a file >of type "zz-application/zz-winassoc-pdb". Since your site works >perfectly (nice rotatable molecule) I _know_ I have the plug-in. I have >also checked the Netscape plug-in info, and the Chime plug-in is in >there, and is enabled. > >What am I missing? Why does my plug-in work for your file on your site, >but not for your file on my hard drive? > >John de Banzie (Assoc. Prof. Biology) > >debanzie@cherokee.nsuok.edu Dear Dr. de Banzie: You've got me stumped. I never heard of those zz MIME types before. Is this with Win95? Occasionally people have had bizzare problems which went away when they uninstalled and then reinstalled Navigator and Chime. That is all I can suggest. I assume you're using Navigator's File menu to Open Page (Open in Nav3) the index.htm file? Sometimes if people spell out EXACTLY what they are doing and versions of all software we can spot something you are doing wrong which we took for granted with a less detailed account. I've copied this to the rasmol email list in case someone else has seen these zz MIME types or has a suggestion. (If you don't subscribe, you can see each day's responses after 3 AM EST the following day at http://www.umass.edu/microbio/rasmol/raslist.htm) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page (http://www.umass.edu/microbio/rasmol) - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime resources compatible with Nav 3.0x again Date: Thu, 12 Mar 1998 13:31:18 -0500 To: rasmol@dhcp-srv2.oit.umass.edu On February 17 and 19, I added font size control to my Chime presentations on hemoglobin, antibody, and MHC, and to the downloadable template for making new presentations (http://www.umass.edu/microbio/chime). Yesterday Tim Driscoll pointed out that these font size controls don't work properly in Navigator 3.0x and cause it to crash (on both Windows 95 and Macintosh). I have therefore disabled font size control when these are viewed in Nav 3.0x. All other features work fine in Nav 3.0x, and all features including font size control work fine in Nav 4.0x. The change is announced at http://www.umass.edu/microbio/chime/newchime.htm Anyone using the template downloaded since Feb 17 may wish to download the new version and replace the file fontsize.js, which is the only file changed since then. Those who built presentations with the template downloaded before Feb 17 can easily install font size control -- instructions are at http://www.umass.edu/microbio/chime/prsswc/2fc-how.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page (http://www.umass.edu/microbio/rasmol) - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Lee Subject: angles Date: Fri, 13 Mar 1998 13:08:25 -0500 To: "rasmol@lists.umass.edu" Hello Everyone I was wondering if there are any features of the 2.0 beta is plugin which allow interactive viewing of bond angles whereby the angles are displayed directly on the structure rather than in a javascript alert box. Thank you in advance ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Lee Subject: Chime 2.0 and button viewing problems with Internet Explorer 4.0 Date: Fri, 13 Mar 1998 15:04:27 -0500 To: "rasmol@lists.umass.edu" Has anyone had any problems with chime 2.0 and Internet Explorer 4.0 where a page containing embeded chime scripts with buttons do not view correctly at first but are ok after reloading the page. The problem I am seeing specfically involves the appearance of phantom buttons when the page is first loaded. Any help would be greatly appreciated. ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Lee Subject: Is there a newsgroup for rasmol and/or chime? Date: Fri, 13 Mar 1998 15:05:52 -0500 To: "rasmol@lists.umass.edu" ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime: IE4, angles, script completion Date: Fri, 13 Mar 1998 04:21:07 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Adrian Lee asked several questions: 1. QUESTION: IE4 Has anyone had any problems with chime 2.0 and Internet Explorer 4.0 where a page containing embeded chime scripts with buttons do not view correctly at first but are ok after reloading the page. The problem I am seeing specfically involves the appearance of phantom buttons when the page is first loaded. Any help would be greatly appreciated. MY REPLY: I have not heard from anyone at MDL that IE4 is fully compatible with Chime. I doubt that it is. Therefore I strongly recommend using Navigator. Navigator version 3 is fine with Chime version 1, but if you are using Chime 2 beta, use Navigator 4.04. Again, the problem here is not a lack of support for IE from MDL; it is that Chime is a plugin, Netscape defined the plugin protocol, and IE has not yet provided full plugin compatibility. 2. QUESTION: ANGLES I was wondering if there are any features of the 2.0 beta is plugin which allow interactive viewing of bond angles whereby the angles are displayed directly on the structure rather than in a javascript alert box. MY REPLY: Not that I know about. The message call back mechanism allows you to do something other than put the angle report in a javascript alert box. For example you could create a nicely formatted report document in a separate frame. But I don't think there is any way to get the angle displayed in the graphic (as there is for distances using the monitor commands). 3. QUESTION (SCRIPT POPUP) The new plugin likes to tell you when a script is completed by giving you an annoying popup dialogue box. Is there any way around this other than disabling Javascript? In Internet Explorer 4.0 Javascripts can not be disabled like they can in Netscape. Does anyone have any suggestions? MY REPLY: I would need to know what url you are looking at. My sites have error trapping code which puts any unexpected messages in an alert box. When Chime 2 beta first became available, it had additional script completion messages which caused such alerts. I believe I have fixed my url's so that problem is gone. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page (http://www.umass.edu/microbio/rasmol) - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id RAA20073 ++++------+------+------+------+------+------+------+------+------+------+ From: Shaun Landau Subject: Chime pages don't view properly with my Web Server Date: Fri, 13 Mar 1998 17:47:48 -0500 To: "'Rasmol'" I have created some html pages which work fine when accessed by Netscape as local files. I also have a Web server (Microsoft Personal Webserver) running on my machine. When I try to access these same pages via http, i.e. through TCPIP in conjunction with my web server, my Netscape browser seems to not know what to do with the chime graphics even though the plugin has been properly installed. This is clearly not a problem with Netscape but seems to rather be a problem with my server. Are there any settings or extension I must modify on my server in order for people to properly access chime pages? Any insights would be greatly appreciated. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime pages don't view properly with my Web Server Date: Fri, 13 Mar 1998 05:26:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu At 05:47 PM 3/13/98 -0500, you wrote: > I have created some html pages which work fine when accessed by Netscape as local files. I also have a Web server (Microsoft Personal Webserver) running on my machine. When I try to access these same pages via http, i.e. through TCPIP in conjunction with my web server, my Netscape browser seems to not know what to do with the chime graphics even though the plugin has been properly installed. This is clearly not a problem with Netscape but seems to rather be a problem with my server. Are there any settings or extension I must modify on my server in order for people to properly access chime pages? Any insights would be greatly appreciated. This is a frequently asked question. The answer is on Chime's FAQ page at http://www.mdli.com/chemscape/chime/chimehelp.html#Trouble1 and is also mentioned on my site, e.g. at Presenting RasMol-Saved Scripts with Chime, then How to Install Your Scripts into the Chime Template (see last few steps) http://www.umass.edu/microbio/chime/prsswc/2fc-how.htm and Programming Chime web pages from scratch http://www.umass.edu/microbio/chime/chimehow/chimake.htm Your server needs to be configured to serve .pdb as chemical/x-pdb, and .spt as application/x-spt. If you use any javascript files, also .js as application/x-javascript. Otherwise, Navigator doesn't know what to do with the files (except in local mode). /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page (http://www.umass.edu/microbio/rasmol) - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Shaun Landau Subject: RE: Chime: IE4, angles, script completion Date: Fri, 13 Mar 1998 21:55:56 -0500 To: "'rasmol@lists.umass.edu'" ------ =_NextPart_000_01BD4ECA.CE479540 I am designing my own pages with embedded chime scripts. How did you = work around the chime 2.0 Javascript alerts and error messages? Is it a = matter of simply adding some html code to the pages? -----Original Message----- Sent: Friday, March 13, 1998 4:21 AM From: Eric Martz [SMTP:emartz@microbio.umass.edu] Subject: Chime: IE4, angles, script completion To: rasmol@dhcp-srv2.oit.umass.edu The new plugin likes to tell you when a script is completed by giving you an annoying popup dialogue box. Is there any way around this other than disabling Javascript? In Internet Explorer 4.0 Javascripts can not be disabled like they can in Netscape. Does anyone have any suggestions? MY REPLY: I would need to know what url you are looking at. My sites have error trapping code which puts any unexpected messages in an alert box. When Chime 2 beta first became available, it had additional script = completion messages which caused such alerts. I believe I have fixed my url's so = that problem is gone. ++++------+------+------+------+------+------+------+------+------+------+ From: "Donald W. Low" Subject: potential surfaces Date: Fri, 27 Mar 1998 13:53:15 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Hello all I tried my best to see if this topic had been covered in the history, so forgive me if it has. The question I have concerns coloring dot surfaces with the gradient color scheme for electrostatic potential. I'm using V 2.6 UCB, and I can get my residues (and their corresponding dots) to be color coded by potential, but when I try to make the graded potential surface it just ends up giving me a uniformly red surface. Any ideas? thanks - Don Low Gryphon Sciences, USA ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: potential surfaces Date: Wed, 01 Apr 1998 16:01:30 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I suggest that you try out Chime 2, which automatically generates solid or transparent surfaces (not only dot surfaces) and colors them automatically by electrostatic potential. www.mdli.com/download/chime At 3/27/98 , you wrote: > >Hello all > >I tried my best to see if this topic had been covered in the history, so >forgive me if it has. > >The question I have concerns coloring dot surfaces with the gradient color >scheme for electrostatic potential. I'm using V 2.6 UCB, and I can get my >residues (and their corresponding dots) to be color coded by potential, >but when I try to make the graded potential surface it just ends up giving >me a uniformly red surface. Any ideas? > >thanks > >- Don Low > >Gryphon Sciences, USA > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page (http://www.umass.edu/microbio/rasmol) - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Future of RasMol Date: Sun, 05 Apr 1998 14:26:15 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Dear Rasmolians: During recent months, you may have noticed the absence, on this email list, of Roger Sayle's authoritative responses to questions about his creation, RasMol. Roger departed from GlaxoWellcome in December, 1997, and is now residing in the United States, involved in a startup software company. It appears unlikely that Roger will make future contributions to RasMol. Inquiries of the people with whom Roger worked at GlaxoWellcome have yielded no evidence of plans for further development of RasMol there. Perhaps volunteers will emerge to improve RasMol, and to compile executables for Windows95 and Macintosh. This email list would be an appropriate medium for coordinating such efforts. Volunteers to improve the documentation would also be welcome. It turns out that Roger had a sophisticated system for converting the master reference manual into html, postscript, and the on-line format available from RasMol's Help menu. Unfortunately, this came to light after Margaret Wong and I had already updated the html copy to version 2.6. Were volunteers to emerge, perhaps the documentation management software could be obtained from Roger and the html manual restored back to this system. Is there a need for further development of RasMol? RasMol is surely in use by hundreds of thousands of people. RasMol's unique strengths include its engaging interface, the high quality and beauty of its renderings, and its astonishing speed in rotating spacefilled or cartoon images. On the one hand, improved versions would likely be used by thousands. On the other hand, Chime has inherited nearly all of RasMol's strengths and added many powerful features. Chime version one, and especially the html interfaces for it currently on the web, largely lack the capability for self-directed exploration of any molecule present on the client's hard disk. They also lack RasMol's powerful 'save script' mechanism for playing back carefully constructed renderings. This is changing. Chime version two makes possible nearly all of RasMol's strengths in an even more user-friendly interface, and much more. Although not yet released, completion of Chime 2 is receiving intense effort from the staff at MDL. Loading molecules from the client's hard disk (see example and saving scripts are straightforward in Chime 2. Indeed, most of the limitations of scripts saved by RasMol (see ), including the absolute pathname in the load command which fails when the script is moved, have been fixed in Chime 2, thanks to the care and attention of Tim Maffett and Bryan van Vliet of MDL's Chemscape team. New html interfaces need to be developed before these capabilities are delivered in an optimal way, but these will likely be forthcoming in the near future. It seems likely that Chime and these new web interfaces will supercede RasMol for most purposes, though it will undoubtedly take many years to convert the large established user-base of RasMol. Roger's extraordinary generosity in putting RasMol and its source code in the public domain has borne fruit. RasMol now has two freeware children (Chime and Weblab) which incorporate key parts of Roger's brilliant source code. There is also one freeware grandchild, a portion of Sculpt bundled with Chime 2. In closing, since Roger appears to be bowing out, I would like to thank Roger for his phenomenal contribution to science education and his years of tireless support of RasMol, and to wish him luck and happiness in his new ventures. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu UMass Chime Site - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <0EQY00H1JGRCDW@rfd1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Peter C. McCluskey" Subject: DisMol - an applet with many RasMol features (Re: Future of RasMol) Date: Mon, 6 Apr 1998 09:14:46 -0700 To: rasmol@dhcp-srv2.oit.umass.edu emartz@microbio.umass.edu (Eric Martz) writes: >Roger's extraordinary generosity in putting RasMol and its source code in >the public domain has borne fruit. RasMol now has two freeware children >(Chime and Weblab) which incorporate key parts of Roger's brilliant source >code. Make that three. I've got a Java applet at http://www.rahul.net/pcm/dismol/DisMol.html that originally started out as an enhancement to Will Ware's NanoCAD applet, but I keep finding reasons to port more RasMol code to Java to enable it to handle large molecules adequately. Currently it's only advantage over RasMol/Chime is that you can use it to show others your molecules without requiring they install anything more than a standard browser. I don't have any clear plans for further changes to this code, but I hope to experiment with it as a UI for something like MMTK (http://starship.skyport.net/crew/hinsen/mmtk.html) or Tinker. -- ------------------------------------------------------------------------ Peter McCluskey | Critmail (http://crit.org/critmail.html): http://www.rahul.net/pcm | Accept nothing less to archive your mailing list ++++------+------+------+------+------+------+------+------+------+------+ From: Toni Kazic Subject: Re: Future of RasMol Date: Mon, 6 Apr 1998 18:16:47 -0500 (CDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Dear all, I hope Roger reads this list (or Eric can provide a forwarding email) long enough to receive his richly deserved praise and thanks. To that I add my voice ----- T H A N K S R O G E R AND G O O D L U C K!!!!!!!!!!!! Toni Toni Kazic, Ph.D. Institute for Biomedical Computing Box 8036 Washington University 700 South Euclid Ave. St. Louis MO 63110 314-362-3121 (vox) 314-362-0234 (fax) toni@athe.wustl.edu http://ibc.wustl.edu/~toni References: <0EQY00H1JGRCDW@rfd1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: Future of RasMol Date: Mon, 06 Apr 1998 22:12:55 +0200 To: rasmol@dhcp-srv2.oit.umass.edu One question: Can we expect a improved version of Rasmol with POVRay-output in the future (as it has been announced aproximately half a year ago)??? Anyone still working on an improved Rasmol-version?? -- Bye, Marc Saric Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/ Visit the FS98 3D-accelerators FAQ at http://www.simflight.com/marc -----BEGIN PGP SIGNATURE----- Version: PGP for Personal Privacy 5.0 Charset: noconv iQA/AwUBNMp1DRQHQPcpGdKHEQJJKQCg7rXNo2cf2KAxX4G1Dx5JoEIZNpkAn1zH vlnrohT9/RjfjlyjfNa7prUD =C/ql -----END PGP SIGNATURE----- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Future of RasMol Date: Tue, 7 Apr 1998 17:34:34 -0600 (MDT) To: rasmol@dhcp-srv2.oit.umass.edu On Mon, 6 Apr 1998, Marc Saric wrote: > One question: Can we expect a improved version of Rasmol with > POVRay-output in the future (as it has been announced aproximately half > a year ago)??? > > Anyone still working on an improved Rasmol-version?? Arne Mueller with the Institut fuer Molekulare Genetik at the Univerity of Goettingen will shortly be making his patches to RasMol available as version 2.6x1, which includes improved support for POV-ray output. Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ 419 East Palace Avenue, Tel: (+1) 505-984-0613 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Noncovalent Bond Finder w/ Chime 2 Date: Wed, 08 Apr 1998 12:36:29 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Dear Chimeleons: I have developed an experimental Chime interface for quickly finding noncovalent bonds, namely atom pairs between chains, or chains and ligands, at suitable distances for hydrogen bonding or hydrophobic bonding. It is really easy to use (I hope!): you just load a PDB file from your computer (automatic browse interface and load button), or one of the samples provided, select a chain, ligand, or other moiety (any desired set of atoms), and push a button. The closest atoms to your target set are highlighted. Repeated button pushes move the finding shell out in 0.1 Angstrom increments. There is a tutorial demonstration on how to use it, and lots of help, including a very basic intro to hydrogen bonds complete with GIFs. The Noncovalent Bond Finder REQUIRES Chime 2 (beta 2 is fine) and Navigator 4 (4.04 recommended). As has been discussed here previously, Chime 2 beta is not yet available for the Macintosh (MDL is working hard on this as we speak ...), and will NOT be developed for Win 3.1. Therefore, you can only do this on Win95 at the moment. Try it at As always, you can download it for local use. (It took me 2 days of intense effort from start to 'finish', tho I doubt that it's 'finished'. My wife commented that I looked like a statue. :-) Let me know what you think. Please point out any misleading statements or errors (I am not a hard-core chemist!). Have fun, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu RasMol Home Page (http://www.umass.edu/microbio/rasmol) - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: Future of RasMol Date: Wed, 08 Apr 1998 19:46:48 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Roger Sayle wrote: > Arne Mueller with the Institut fuer Molekulare Genetik at the > Univerity of Goettingen will shortly be making his > patches to RasMol available as version 2.6x1, which includes improved > support for POV-ray output. Thanks for the info! And thanks again for the great program -and good luck for the future! -- Bye, Marc Saric Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/ Visit the FS98 3D-accelerators FAQ at http://www.simflight.com/marc -----BEGIN PGP SIGNATURE----- Version: PGP for Personal Privacy 5.0 Charset: noconv iQA/AwUBNMp1DRQHQPcpGdKHEQJJKQCg7rXNo2cf2KAxX4G1Dx5JoEIZNpkAn1zH vlnrohT9/RjfjlyjfNa7prUD =C/ql -----END PGP SIGNATURE----- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Noncovalent Bond Finder Upgraded Date: Sun, 12 Apr 1998 23:22:00 -0400 To: rasmol@dhcp-srv2.oit.umass.edu My noncovalent bond finder has been further enhanced (now version 1.2). In particular, it should no longer crash Navigator constantly. Also some handy new capabilities were added. More enhancements are planned. If you have suggestions, please let me know. http://www.umass.edu/microbio/chime/find-ncb/index.htm /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu UMass Chime Site - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Most popular uses of the RasMol Home Page. Date: Sun, 12 Apr 1998 23:33:35 -0400 To: rasmol@dhcp-srv2.oit.umass.edu This week (ending 4/11/98), I determined the numbers of accesses to individual pages at the RasMol Home Page web site. There were a total of 4,024 visitors (unique IP addresses) during the 7-day period, consistent with the past 5 weeks. These visitors fetched 78,792 files during the 7-day period. Most of our visitors are interested in getting RasMol, and over 1,000/week download the program (consistent with last year's 41,000 total downloads). The second most popular use is finding PDB files (940 people), and use of our new simplified PDB search interface is the 5th most popular activity at the site (438 people). Third most popular is the RasMol Quick Start document (888 people), and fourth, the gallery (500 people). 327 people consulted the RasMol reference manual. While 265 people looked at the RasMol "movie" script page, only 67 scripts were downloaded. If this keeps up, there will be over 3,000 "movie" script downloads for the year, comparable to last year's 4,500 downloads. Since I regard the "movie" script as an obsolete format, I was pleased that there were 155 downloads of Chime packages, greater