++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Hello world! Date: Thu, 02 Jan 1997 19:35:54 +0100 To: rasmol@noc1.oit.umass.edu Hi All! Iīm new to the RASMOL discussion-list and want to intoduce myself (and test the connection at the same time :-): My name is Marc Saric, I am 25 years old and live in Essen, Germany. I study Biology at the Ruhr-University of Bochum. http://www.ruhr-uni-bochum.de Iīm interested in molecular dynamics simulation and bochemical computer graphics (although I donīt know much about the physicīs underlying things like "Potential Energy Surfaces" and "Forcefields" or about programming and computer sciences). I have started to use RASMOL aprox. 1 1/2 year ago (after I got my Internet-account and found the program on the net), and have some minor experiences with InsightII and GROMOS, which I used during a course at the university (Lehrstuhl fuer Biophysik, Univerity of Bochum). Thatīs all for now! Happy New Year to everyone! -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/index.htm ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: ProtSecS & linear presentation structure for Chime 1.0 Date: Fri, 3 Jan 1997 11:43:25 -0500 (EST) To: rasmol@noc1.oit.umass.edu A new version of my short elementary Chime tutorial on protein secondary structure is now available at http://www.umass.edu/microbio/chime It has been thoroughly tested for Windows 3.1 and Windows 95 but may require some fine-tuning for Macintosh or SGI. I will soon be able to do Macintosh tests myself. However, I won't do SGI tests myself. If you find problems (particularly with the layout of the debug screen) a GIF snapshot of the screen would be a significant help to me (ftp to marlin.bio.umass.edu/incoming; please do not attach to email). Chime 1.0 was released for all platforms on December 31, 1996. Tim Maffett, principal architect of Chime, was kind enough to share pre-release versions with me which allowed me to work on a new html/javascript control structure for linear presentations in Chime, using my short elementary tutorial on protein secondary structure for content. For those interested in developing linear presentations with Chime, I have provided detailed instructions on how to put your own content into what I call 'linear control structure version 2' (LCS2) for Chime presentations. Existing RasMol scripts or linear Chime scripts can of course be inserted into LCS2. The web site provides mechanisms for downloading the 60-some files which comprise LCS2 with the protein secondary structure Chime-scripts. Once you have downloaded a private copy, you can play the tutorial, examine its construction, and insert your own content, all using Netscape 3.01 to display local files without an Internet connection. Version 1, available since November 6, already provided the ability to enter the Chime-script at any desired section, to replay a section (backing up), and to cancel play at any point. These features have been retained and improved. LCS2 and Chime have abolished the 'press any key' mechanism of releasing a pause in a RasMol/Chime-script. Pauses are now released by clicking on a button. LCS2 provides a continuous-play mode. This means that a paused Chime-script can also be played continuously from start to finish without needing any button clicking to continue. Chime has a new command 'javascript'. This means that the contents of the legend frame can now be changed directly by the Chime-script itself using javascript calls. LCS2 also provides a development/debugging mode which displays each Chime-script command line as it is executed, monitors which script or subscript file is executing, and provides several trace modes (new script files, single-step tracing, or tracing of any desired command). When a traced event occurs, you have the options of continuing the Chime-script with tracing on, continuing with tracing off, or interrupting the script. After an interrupt, the command-line interface allows you to type commands manually to test possible modifications to the script command sequence. LCS2 consists of about 1,000 lines of javascript plus over 800 lines of html (excluding the design/methods document and blank lines). The protein secondary structure Chime-script itself is 440-some commands in length, and runs about 5 minutes if played continuously without pausing. However, a script of any length can be presented with LCS2. Happy new year! /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ X-Nextstep-Mailer: Mail 3.3 (Enhance 1.3) ++++------+------+------+------+------+------+------+------+------+------+ From: Vicki Bragin Subject: Need help from NEXTSTEP Rasmol users ! Date: Fri, 3 Jan 97 10:55:23 -0800 To: rasmol@noc1.oit.umass.edu Cc: vbragin@ix.netcom.com --NeXT-Mail-1821844478-1 Are there any NEXTSTEP Rasmol users out there who might be willing = to help recompile the NEXTSTEP version so as to add the picking = functionality, and perhpas other capabilities as well which I may = not even be aware of and which have not been updated on the = NEXTSTEP version. For starters, I thought I would first try to = compile the code as is. I downloaded the source code, compiled it = on my Pentium Intel running NEXTSTEP 3.3, then loaded a pdb file, = but no graphics appears in the graphics window at all. =20 Some detail: In response to the error message, rasmol.c: In function `ras_init': rasmol.c:1047: warning: braces around scalar initializer I replaced the braces with (). The app compiled fine but, still, = no graphics on the window. rasmol.h: I changed the user-defined options from #define TWOBIT to #define SIXTEENBIT=20 Anything that I may have missed? Thanks. ********************************************************** Victoria M. Bragin Physical Sciences Division, Pasadena City College 1570 E. Colorado Blvd., Pasadena, CA 91106-2003 Phone: (818) 585-7147 Fax: (818) 585-7919 E-mail: (NeXTmail and MIME mail welcome) vbragin@nextlab.calstatela.edu vbragin@ix.netcom.com vbragin@paccd.cc.ca.us vbragin@pslc.ucla.edu ********************************************************** --NeXT-Mail-1821844478-1 Are there any NEXTSTEP Rasmol users out there who might be willing = to help recompile the NEXTSTEP version so as to add the picking = functionality, and perhpas other capabilities as well which I may = not even be aware of and which have not been updated on the = NEXTSTEP version. For starters, I thought I would first try to = compile the code as is. I downloaded the source code, compiled it = on my Pentium Intel running NEXTSTEP 3.3, then loaded a pdb file, = but no graphics appears in the graphics window at all. =20 Some detail: In response to the error message, =09 rasmol.c: In function `ras_init': rasmol.c:1047: warning: braces around scalar initializer I replaced the braces with (). The app compiled fine but, still, = no graphics on the window. rasmol.h: I changed the user-defined options from #define TWOBIT to #define SIXTEENBIT=20 Anything that I may have missed? Thanks. ********************************************************** Victoria M. Bragin Physical Sciences Division, Pasadena City College 1570 E. Colorado Blvd., Pasadena, CA 91106-2003 Phone: (818) 585-7147 Fax: (818) 585-7919 E-mail: (NeXTmail and MIME mail welcome) vbragin@nextlab.calstatela.edu vbragin@ix.netcom.com vbragin@paccd.cc.ca.us vbragin@pslc.ucla.edu ********************************************************** --NeXT-Mail-1821844478-1-- X-Nextstep-Mailer: Mail 3.3 (Enhance 1.3) ++++------+------+------+------+------+------+------+------+------+------+ From: Vicki Bragin Subject: RasMol for NEXTSTEP able to run as many molecules as desired Date: Sun, 5 Jan 97 22:59:35 -0800 To: rasmol@noc1.oit.umass.edu Cc: vbragin@ix.netcom.com For NEXTSTEP users of RasMol, one can load as many molecules as = desired in as many windows and move them independently - no = additional code is needed. One is limited only by the = impracticality of having too many windows running RasMol = simultaneously! Simply create as many links to the original = application as desired and run the applications independently. = For example, to enable simultaneous display of 3 different = molecules and be able to move them independently, create 2 links = to the original application, locate these links in different = directories, and position the graphics viewer any where on the = screen such that all 3 windows are simultaneously visible. I use = this method to have my students run a script on one window, have = them load two different sample molecules on the other windows = while the script is paused (or even while it is running), = manipulate them independenty, ... and thus be able to make beter = comparisons of structures. I imagine this must be true for all = UNIX versions of RasMol due to UNIX multitasking capability. =20 Vicki Bragin ********************************************************** Victoria M. Bragin Physical Sciences Division, Pasadena City College 1570 E. Colorado Blvd., Pasadena, CA 91106-2003 Phone: (818) 585-7147 Fax: (818) 585-7919 E-mail: (NeXTmail and MIME mail welcome) vbragin@nextlab.calstatela.edu vbragin@ix.netcom.com vbragin@paccd.cc.ca.us vbragin@pslc.ucla.edu ********************************************************** desired ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: RasMol for NEXTSTEP able to run as many molecules as Date: Mon, 6 Jan 1997 12:02:59 -0500 (EST) To: vbragin@ix.netcom.com Cc: rasmol@noc1.oit.umass.edu On 1/5/97 Vicki Bragin wrote: >For NEXTSTEP users of RasMol, one can load as many molecules as desired in as >many windows and move them independently - no additional code is needed. One could also achieve what Vicki describes with Chime, using multiple Chime invocations on the same web page. You could, for example, run a script up to a pause on one plug-in graphic, while offering a command-line interface on another plug-in graphic side by side. It would be more work (html/javascript programming) than with the NextStep/unix approach, but with the advantage that the layout of the plug-ins ('windows' ) etc. would be defined by the html, and would not have to be manually re-established each time (as with RasMol). Also, you can surround the graphic 'windows' with whatever text/explanation (even in a separately scrolling frame), with content changed to match what is going on in Chime. Remember, now Chime has a javascript command so Chime-scripts can do anything you want to the web page, including change the content of other frames. (See http://www.umass.edu/microbio/chime/protsecs/index.htm for an example of the use of javascript in .spt files to change content of a legend frame.) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: vasil@iabunix.iab.ac.ru Subject: RasMol for Linux Date: Thu, 9 Jan 1997 19:18:15 +0000 To: rasmol@noc1.oit.umass.edu Hi, Do somebody hear about RasMol for Linux Slackware? If you know about such version, please, help me. Sergey Vasil'ev Computer Modeling Group Institute of Agricultural BioTechnology Moscow, Russia ++++------+------+------+------+------+------+------+------+------+------+ From: "Francis M.J. Hsieh" Subject: Re: RasMol for Linux Date: Fri, 10 Jan 1997 01:02:19 +0800 (WST) To: rasmol@noc1.oit.umass.edu > Do somebody hear about RasMol for Linux Slackware? > If you know about such version, please, help me. > > Sergey Vasil'ev You can get the unix source code and compile it directly. -- Francis M.J. Hsieh | email: mjhsieh@life.nthu.edu.tw Graduate student at Dept. of Life | Homepage: Science, National TsingHua Univ., | http://life.nthu.edu.tw/~mjhsieh/ Taiwan. | TEL: +886 3 5715131 ext 3482 ++++------+------+------+------+------+------+------+------+------+------+ From: Andrea Bernini Subject: Re: RasMol for Linux Date: Sat, 11 Jan 1997 10:41:20 +0100 (GMT+0100) To: rasmol@noc1.oit.umass.edu On Thu, 9 Jan 1997 vasil@iabunix.iab.ac.ru wrote: > Hi, > > Do somebody hear about RasMol for Linux Slackware? > If you know about such version, please, help me. > > Sergey Vasil'ev > > Computer Modeling Group > Institute of Agricultural BioTechnology > Moscow, Russia > Hi Sergey, to install RasMol 2.6 beta2 on linux you have to get the source package RasMol26b2.tar.gz placed in ftp://marlin.bio.umass.edu/pub/shareware/rasmol/distrib/ then you have to compile it. Andrea Bernini, Dep. Molecular Biology, University of Siena, Italy References: <199701091623.LAA03476@noc1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: RasMol for Linux Date: Sun, 12 Jan 1997 15:33:09 +0100 To: rasmol@noc1.oit.umass.edu vasil@iabunix.iab.ac.ru wrote: > Do somebody hear about RasMol for Linux Slackware? > If you know about such version, please, help me. You have to get the source-code (as you allready should know from the other mails), but it only works with monochrome, 8 or 24bit X-Window-Displays, no other (unfortunately). Maybe this will change in future versions. -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/index.htm ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMol for Linux Date: Sun, 12 Jan 1997 16:45:42 +0000 (GMT) To: Marc Saric Cc: rasmol@noc1.oit.umass.edu Hi Marc, > > Do somebody hear about RasMol for Linux Slackware? > > If you know about such version, please, help me. > You have to get the source-code (as you allready should know from the > other mails), but it only works with monochrome, 8 or 24bit > X-Window-Displays, no other (unfortunately). Maybe this will change in > future versions. You'll be pleased to hear that the currently distributed version of RasMol will also support 16bit per pixel displays as a compile time option. This should help those Linux users that have configured the latest version of the XFree server with "-16bpp". When configuring "rasmol.h" or the Makefile, simply specify "#define SIXTEENBIT" rather than EIGHTBIT or THIRTYTWOBIT. I hope this helps. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 theurer@student.umass.edu, bev@cs.umass.edu, ehaugsja@cs.umass.edu, dhart@cs.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime DNA Tutorial enhanced Date: Tue, 21 Jan 1997 09:03:21 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: cfinlays@elux3.cs.umass.edu, theurer@student.umass.edu, I have placed an enhanced version of my nonlinear Chime tutorial on DNA structure at http://www.umass.edu/microbio/chime This version shows much more detail on single AT and GC base pairs, including double bonds. You can toggle on and off hydrogen atoms. A development/debugging mode has been implemented. Many of the moves now take full advantage of Chime 1.0's simultaneous XYZ rotation/translation/zoom capability. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Save RasMol's Windows Sizes/Positions! Date: Wed, 22 Jan 1997 22:17:59 -0500 (EST) To: rasmol@noc1.oit.umass.edu I just discovered an amazing shareware program for Windows 3.1 (ONLY, not Win95). It makes RasMol (or most other programs) startup with the same windows sizes and positions (both windows!) as when you last closed it. Get FreezeFrame file FF.ZIP from e.g. http://filepile.com. Use Windows File, New to create an icon for it. Double click the icon and a minimized icon will appear at the bottom of your screen. Startup RasMol, resize/reposition the windows, and close RasMol. Now start it up again and Voila! FF remembers the window settings between sessions. Just start it up before RasMol and you get the same window sizes/positions every time. Oh what a relief it is!! Use Write to view the help file FF.WRI if you wish. Let's each send this guy the $5 he asks for, and maybe he can be persuaded to make a Windows 95 version! Send your check payable to Ronald Crane to: FreezeFrame Registration c/o Ronald Crane 758 Vasona St. Milpitas, California 95035-4316 I could not find this gentleman nor his product by searching AltaVista. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Gryko Subject: displaying crystals Date: Mon, 3 Feb 1997 15:30:31 -0700 To: "'rasmol1'" Hello: I need to display unit cell of a crystal. Any hints how to do this in Rasmol? Of course, I can put dummy atoms at cell vertices and draw all conncting lines but maybe there is a better way to do this. Thanks, Jan Gryko College of Eastern Utah ++++------+------+------+------+------+------+------+------+------+------+ From: Hidehiro UEKUSA Subject: Re: displaying crystals Date: Tue, 04 Feb 1997 11:49:21 +0900 To: rasmol@noc1.oit.umass.edu Hi Jan, In message you write: > > Hello: > > I need to display unit cell of a crystal. Any hints how to do this in >Rasmol? I usually do that by inserting 'CRYST1' line in a PDB format data file and use 'set unitcell on' command in rasmol. 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). I hope this would help you. ---------------------------------------------------------------- Hidehiro UEKUSA (uekusa@chem.titech.ac.jp) Department of Chemistry, Tokyo Institute of Technology, JAPAN ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: 2 Chime questions Date: Tue, 4 Feb 1997 17:27:32 +0000 To: rasmol@noc1.oit.umass.edu Now that Chime rotates so fast, is there a simple command to control the speed of rotation? Also, sorry I forgot, but to ensure lack of palette problems with Windows browsers and Chime, is the command I should include "palette=foreground" or vice a versa? TIA _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html ++++------+------+------+------+------+------+------+------+------+------+ From: "Mike Fearn" Subject: rasmol default display mode Date: Tue, 4 Feb 1997 17:58:40 +0000 To: rasmol@noc1.oit.umass.edu On the Unix version of rasmol, can I insert a command in my .rasmolrc which will ensure the initial display mode is set to 'Ball & Stick' ? Regards, Mike Fearn. -- ------------------------------------------------------------------- | Mike Fearn, Tel : UK (01684) 896536 | | Room PA101, Fax : UK (01684) 896150 | | D.R.A, Malvern, | | Worcs. WR14 3PS Email : hp003@dra.hmg.gb | ------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: RE: 2 Chime questions Date: Tue, 4 Feb 1997 12:57:32 -0500 (EST) To: rasmol@noc1.oit.umass.edu In message Tue, 4 Feb 1997 17:27:32 +0000, Fergus Doherty writes: > Now that Chime rotates so fast, is there a simple command to control the > speed of rotation? Yes. See the draft Chime manual on the 'move' command. http://www.umass.edu/microbio/chime/manual/chimeman.htm > Also, sorry I forgot, but to ensure lack of palette problems with Windows > browsers and Chime, is the command I should include "palette=foreground" > or vice a versa? I don't use this. In my tutorials, I need colors in the legend frame color key to remain true. On a 256-color Windows platform, forcing the Chime palette sometimes causes colors in another frame to be incorrect. I haven't had time to find out whether this problem can be avoided if I use legend colors which are exactly the same rgb value as the nominal color in the Chime frame. For this purpose, it would be helpful if Roger Sayle or Tim Maffett could post on this list the starting RGB values used for the CPK color scheme and secondary structure color schemes. Presumably they could be found in the source code to RasMol (ported to Chime), but I haven't managed to look for them there yet. -Eric /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Mitchell Miller Subject: Re: 2 Chime questions Date: Tue, 4 Feb 1997 12:15:34 -0800 To: rasmol@noc1.oit.umass.edu Cc: Chime-feedback@mdli.com Hello Fergus, You can control the speed of continuous rotation of a Chime structure by coding spiny= to rotate about the Y axis or spinx= to rotate about the X axis or spinz= to rotate about the Z axis. Combinations are also valid. This goes within the tag and may be simpler than writing a script using 'move.' Nevertheless, move is a far more powerful commmand! Hope this helps! Mitch Miller At 09:27 AM 2/4/97 -0800, Fergus Doherty wrote: >Now that Chime rotates so fast, is there a simple command to control the >speed of rotation? > >Also, sorry I forgot, but to ensure lack of palette problems with Windows >browsers and Chime, is the command I should include "palette=foreground" or >vice a versa? > >TIA > > >_____________________________________________________________________ >Fergus Doherty PhD >Dept. Biochemistry, >University Medical School, >Queen's Medical Centre, >Nottingham NG7 2UH > >e-mail: Fergus.Doherty@nottingham.ac.uk >Tel: 0115 970 9366 >FAX: 0115 942 2225 >URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html > > > Mitchell Miller MDL Information Systems, Inc. (801) 569-1390 VoiceMail (800)955-0051 ext. 2163 mitch@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: RE: 2 Chime questions Date: Tue, 04 Feb 1997 14:16:26 -0800 To: emartz@microbio.umass.edu, rasmol@noc1.oit.umass.edu At 09:57 AM 2/4/97 -0800, Eric Martz wrote: >In message Tue, 4 Feb 1997 17:27:32 +0000, > Fergus Doherty writes: > >> Now that Chime rotates so fast, is there a simple command to control the >> speed of rotation? > >Yes. See the draft Chime manual on the 'move' command. >http://www.umass.edu/microbio/chime/manual/chimeman.htm You can also use tag options to change some the degrees per second for each axis. The default is 360 on the Y axis if nothing is specified, and this is TOO MUCH in the new version of Chime. A much more reasonable value is 120 degrees, and in the next version of Chime I will make that the default if nothing is specified. example: The tag parameters that affect rotation are spinY - Y axis rotation in degrees per second (defaults to 360 (too much) if nothing specified for X,Y & Z) spinX - X axis rotation in degrees per second spinZ - Z axis rotation in degress per second spinFPS - the frames per second that Chime will attempt. (note: because of limitations of Win 3.1/95 the max here that you will be able to achieve is ~15. On an NT machine you should be able to get up to 60. NOTE: The rotation commands described above affect only the Chime rotation menu. The Chime script 'Move' command that Eric mentions is a much more precise method of rotation/translation/zoom/slab changes which can be used from the Chime scripting language. > >> Also, sorry I forgot, but to ensure lack of palette problems with Windows >> browsers and Chime, is the command I should include "palette=foreground" >> or vice a versa? > >I don't use this. In my tutorials, I need colors in the legend >frame color key to remain true. On a 256-color Windows platform, >forcing the Chime palette sometimes causes colors in another frame >to be incorrect. I haven't had time to find out whether this problem >can be avoided if I use legend colors which are exactly the same rgb value >as the nominal color in the Chime frame. For this purpose, it would >be helpful if Roger Sayle or Tim Maffett could post on this list >the starting RGB values used for the CPK color scheme and secondary >structure color schemes. Presumably they could be found in the source >code to RasMol (ported to Chime), but I haven't managed to look for >them there yet. One simple trick that you can use is to make your GIF images in other frames use the 'standard 16 windows colors'. The standard 16 windows colors are always available within Windows because they are reserved for things like the window borders and such. The shareware program LView Pro has an option to reduce a GIF image to use only the 16 standard windows colors. On the 'Retouch' menu you should find 'Color Depth...', in this dialog you can select 'Palette Image' and then choose 'Windows Palette (16 colors)'. You can turn on/off dithering to get different results. This method usually works pretty good for simple button images which do not have a wide variety of colors. As far as the Palette values of Rasmol/Chime for the different color settings I do not have them handy, but you can find them defined at the top of 'transfor.c' file within the Rasmol source. You will find array definitions there for the different color settings, and within each of these arrays is the RGB value, along with a comment about what atom type/residue type the color applies to. -tim > >-Eric >/*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 >Molecular visualization: http://www.umass.edu/microbio/rasmol >Immunology: http://www.bio.umass.edu/immunology/immunology.html >Flow cytometry: http://www.bio.umass.edu/mcbfacs >Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 >- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ > > References: <3.0.32.19970204131532.007531c4@bilbo.mdli.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Slaton Subject: RGB values for Rasmol color schemes Date: Tue, 04 Feb 1997 22:20:58 -0800 To: rasmol@noc1.oit.umass.edu This is taken from the very useful Rasmol v2.5 Quick Reference Card (Roger Sayle) included with RasMol 2.5 and 2.6. The file is called "refcard.doc". Hope it's helpful. Colour Schemes -------------- CPK Atom Colours Carbon light grey [200,200,200] Oxygen red [240,0,0] Nitrogen light blue [143,143,255] Hydrogen white [255,255,255] Sulphur yellow [255,200,50] Phosphorous orange [255,165,0] Chlorine green [0,255,0] Calcium, Metals dark grey [128,128,144] Unknown deep pink [255,20,147] Amino Acid Colours ------------------ ASP, GLU bright red [230,10,10] CYS, MET yellow [230,230,0] LYS, ARG blue [20,90,255] SER, THR orange [250,150,0] PHE, TYR mid blue [50,50,170] ASN, GLN cyan [0,220,220] GLY light grey [235,235,235] LEU, VAL, ILE green [15,130,15] ALA dark grey [200,200,200] TRP pink [180,90,180] HIS pale blue [130,130,210] PRO flesh [220,150,130] Secondary Structure Colours --------------------------- Alpha Helix magenta [240,0,128] Beta Sheet yellow [255,255,0] Turns pale blue [96,128,255] Other white [255,255,255] Hydrogen Bond Type Colours -------------------------- Offset +2 white [255,255,255] Offset +3 magenta [255,0,255] Offset +4 red [255,0,0] Offset +5 orange [255,165,0] Offset -3 cyan [0,255,255] Offset -4 green [0,255,0] default yellow [255,255,0] ----------------------------------- Slaton Lipscomb Cabrillo College Aptos, CA ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Gryko Subject: Colors and bonding of "other atoms" Date: Wed, 5 Feb 1997 07:29:06 -0700 To: "'rasmol@lists.umass.edu'" Hello: Sorry, this is probably silly question, but I would like to know how to force Rasmol to color atoms like transition metals and to draw bonds between these atoms. In standard setting Rasmol draws these atoms as nice pink spheres without distinguishing say beteween iron and tungsten and without bonds. Thanks! Jan Gryko, CEU > ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: rasmol default display mode Date: Wed, 5 Feb 1997 15:22:21 +0000 (GMT) To: hp003@dra.hmg.gb Cc: rasmol@noc1.oit.umass.edu Hi Mike, > On the Unix version of rasmol, can I insert a command in my .rasmolrc > which will ensure the initial display mode is set to 'Ball & Stick' ? The ".rasmolrc" initialization file for RasMol is executed after any molecules specified on the command line but before any scripts specified on the command line. Therefore by adding the following commands to the .rasmolrc file: select all spacefill 120 wireframe 40 you should be able to get RasMol to load any files specified on the command line to appear by default as "Ball & Stick". Note that any file loaded explicitly using a "load" command will still appear in wireframe (or backbone) by default. Hence, this technique is only suitable for molecules specified on the command line, such as those launched from Netscape. I hope this helps. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: MS Explorer 3.0 and Chime? Date: Thu, 6 Feb 1997 09:24:39 +0000 To: rasmol@noc1.oit.umass.edu I know earlier versions of Explorer had problems with Chime, but has anyone tried the full release of MIE 3.0? I have tried it on the Mac (a PowerMac 4400, System 7.5.3). MIE loads Chime OK and displays the image, but when I leave that page it crashes (Type 11 - bad news). This happens with my pages and with others. Has anyone else (MacOS or Windows) had problems? _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: MS Explorer 3.0 and Chime? Date: Thu, 6 Feb 97 09:59:23 PST To: rasmol@noc1.oit.umass.edu RasMol/Chime users. In response to Fergus's query below, I was surprised to discover a couple of days ago, on a PC running Windows 95, that the Chime plugin seems to work effectively with the MIE 3.01 browser. Embedded Chime script commands ran correctly, including the new Chime move command. I had no problem with the system crashing (but I have 32 MB RAM). I have not tested the MIE 3.0 browser on my PowerMac 7100, but I am guessing that the problem Fergus has regarding Type II errors is mainly a reflection of insufficient system RAM for running MS applications on a Mac; I've had problems similar to his when launching MS Excel spreadsheets, for example, from Netscape running on a MacIIsi; these problems tended to go away after I converted to a PowerMac 7100 with more RAM. Nevertheless, my initial enthusiasum for using the MIE 3.01 browser for molecular structure presentation waned after I discovered that the push button feature of Chime is not yet implemented. Chime push buttons simply do not appear where I expect to find them on my web pages and no active links could be detected in areas where buttons should have appeared. Thus, given some of the unique HTML possibilities associated with MIE browser, I'm disappointed that it does not yet fully support all of the neat Chime plugin features for scripting molecular structures on the web. Duane At 09:24 AM 2/6/97 +0000, you wrote: >I know earlier versions of Explorer had problems with Chime, but has anyone >tried the full release of MIE 3.0? I have tried it on the Mac (a PowerMac >4400, System 7.5.3). MIE loads Chime OK and displays the image, but when I >leave that page it crashes (Type 11 - bad news). This happens with my pages >and with others. Has anyone else (MacOS or Windows) had problems? > > >_____________________________________________________________________ >Fergus Doherty PhD >Dept. Biochemistry, >University Medical School, >Queen's Medical Centre, >Nottingham NG7 2UH > >e-mail: Fergus.Doherty@nottingham.ac.uk >Tel: 0115 970 9366 >FAX: 0115 942 2225 >URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Duane W. Sears | | Professor of Immunology and Biochemistry | | Department of Molecular, Cell, and Developmental Biology | | University of California Santa Barbara | | Santa Barbara, CA 93106 | | Telephones: | | Office: 805-893-3499 (answering machine) | | Lab: 805-893-4272 | | FAX: 805-893-4724 | | E-mail addresses: | | Faculty: sears@lifesci.lscf.ucsb.edu | | Academic: bioimages@lifesci.lscf.ucsb.edu | | WWW homepages: | | http://mentor.lscf.ucsb.edu/mcdb108a/ | | http://mentor.lscf.ucsb.edu/mcdb133/ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Colors and bonding of "other atoms" Date: Thu, 6 Feb 1997 18:31:47 +0000 (GMT) To: Jan Gryko Cc: rasmol@noc1.oit.umass.edu Hi Jan, > Sorry, this is probably silly question, but I would like to know how > to force Rasmol to color atoms like transition metals and to draw > bonds between these atoms. In standard setting Rasmol draws these > atoms as nice pink spheres without distinguishing say beteween > iron and tungsten and without bonds. Thanks very much for your e-mail. Unfortunately RasMol's CPK colour scheme doesn't ascribe a unique colour to every element in the periodic table and hence most "inorganic" elements tend to be shown in pink. However, it is possible to colour elements individually using commands on the RasMol command line making use of the fact that element names are valid atom expressions. Hence the commands select iron colour green select tungsten colour blue will produce a more colourfull depiction of your molecule. Similarly, RasMol's determination of connectivity is also biased for organic chemistry when displaying large numbers of atoms (i.e. >256). For proteins and nucleic acids, RasMol cheats and uses approximate covalent bonding radii to speed up the calculation. However, more accurate (but often identical) bonds can be found with the connect true command. If this still doesn't improve your heavy atom bonds or your molecule already has less than 250 atoms, the distances between atoms are too large for covalent bonds. Such co-ordination bond are probably best specified by explicitly adding them to the molecular co-ordinate file (i.e. adding CONECT records to a PDB file). I hope this helps. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: RasMol cmds in Chime & new cmds missing in draft manual supports) Date: Fri, 7 Feb 1997 13:54:41 -0500 (EST) To: ------------------------------ Fri, 07 Feb 1997 10:09:41 -0800 From: Tim Maffett Subject: Re: Rasmol commands which Chime 1.0 supports To: Multiple recipients of list Chime 1.0 supports all of the Rasmol command except those that write files to the users disk. (These commands are disabled in Rasmol by default, but can be turned on, they can not be turned on in Chime). In addition the Rasmol 2.6Beta3 commands that Chime supports I have a added some new commands for making it easier to do things like 'movies'/tutorials and such. Some of these commands are included in a 'Draft' Rasmol/Chime reference manual that can be found at: http://www.umass.edu/microbio/chime/ (Eric Martz has some excellent tutorials here that demonstrate many of the Chime specific scripting commands.) This manual is currently incomplete, but it does cover some of the commands I have added since Chime 0.99. Some of the commands which are in Chime 1.0 that are missing from the draft manual are: show version - get version name/number of the rasmol script 'container' (Chime in this case) javascript - sends everything after the 'Javascript' command to be executed by Javascript. examples: javascript if(xyz=5){dosomething();} javascript "image.mypic = 'title.gif'" (This is a powerful command, it allows you do any javascript commands from *within* your Chime/Rasmol script!) status - displays the contents of the quoted string in the Netscape Navigator status bar. (animation commands control XYZ animation files) "show animation", or "animation info" - show anim info "animation" | "anim" - either can be used for command "" can be: "on" - starts animation playing "off" - stops animation "mode" - sets animation mode while playing "loop" - loop from start to end, over and over "once" - loop from start to end ONCE "palindrome" - loop start to end, then end to start over and over "direction" - sets current play direction: "+1" - forward "-1" - backward "fps" "#" of frames per second "info" - prints anim info (see above, you can also use 'show animation" examples: animation mode palindrome animation fps 10 animation direction +1 animation on (Forwarded by ... /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Sergey A. Vasil'ev" Subject: Chime and MS IE 3.01 under Win95 Date: Mon, 10 Feb 1997 19:14:52 +0000 To: rasmol@noc1.oit.umass.edu Hi, I try to install Chime 1.0 on my computer (Windows95 and IE 3.01) but it says that Chime doesn't work without Netscape Navigator. What can I do? Sergey Vasil'ev,M.Sc. Computer Modeling Group, Institute of Agricultural BioTechnology, 42 Timiryazevskaya st., Moscow, 127550, Russia tel. 7(095)211-0509 fax. 7(095)216-4777 e.mail vasil@iabunix.iab.ac.ru vasil@agrobio.msk.su References: <199702101618.LAA02419@noc1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Chris Milne Subject: get Netscape Date: Tue, 11 Feb 1997 00:36:46 -0500 To: rasmol@noc1.oit.umass.edu If you can run I.E. 3.0 you can run Netscape so just download it from www.netscape.com then install the plugin. Other possibility is to just load the file you'd like to view into Rasmol or Web Lab Viewer (if you've got them). Chris Milne Carleton University cmilne@chat.carleton.ca ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: 2D and 3D images with Chime Date: Wed, 12 Feb 1997 13:50:26 +0000 To: rasmol@noc1.oit.umass.edu I know Chime can display .mol files as 2D representations of molecules, and as "3D". But if I create a 2D mol file with ISIDraw this doesn't contain 3D information and the file in "3D" viewed with Chime is flat. A PDB file viewed in Chime on the other hand can only be viewed in 3D. What I want to be able to do is use Chime to load one file (of a small molecule, say cAMP) and view this in 2D, and switch to "real" 3D with the Chime menu. Is this possible, and if so how would I generate the necessary file? If not, is there another way to do it (load mol or pdb files with an embedded script and button)? Finally, how can I generate pdb files from 2D representations of simple molecules - would I need something lke Chem3D to do this? TIA Fergus _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html ++++------+------+------+------+------+------+------+------+------+------+ From: tbender@ccs.carleton.ca (timothy bender) Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 97 18:10:50 EST To: rasmol@noc1.oit.umass.edu ---------------------------------------------------------------------- Tim Bender, B.Sc | To know chemistry, Student, Department of Chemistry | is to know a little Carleton University, Ottawa, Ont, Canada | piece of nature ... Email address: tbender@ccs.carleton.ca | ---------------------------------------------------------------------- Hello ... the newest version of a program called Babel will convert ISISdraw files (.skc) to .pdb files, it is available free of charge from ftp.joplin.biosci.arizona.edu Tim :-) ---------------------------------------------------------------------- "Make something idiot proof and somebody will find a better idiot ..." ++++------+------+------+------+------+------+------+------+------+------+ From: Chris Milne Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 97 18:17:38 EST To: rasmol@noc1.oit.umass.edu You'll need a molecular modelling program like Hyperchem or Chem3d to generate the proper (well maybe not proper, but most likely anyways) 3D coordinates for the structure. These programs will actually minimize the structure using energy calculations (not necessarily all that reliable a calculation). OR : your other option is Web friendly. There's a site hooked to a system called Corina that does molecular modelling for you. You can either enter the molecule into a form on the page (in SMILES format) and submit it, or e-mail them the mol file as text in the message. The site address eludes me now, but it can be found by searching Yahoo's Altavista for 'Corina'. Good luck, ----------------------------------------------------------------------- Chris Milne Carleton University "But then came the day I climbed out of these safe limbs Ventured away Walking tall, head high up, and singing I went to the city Car horns, corners and the gritty Now I am the proudest monkey you've ever seen" - Dave Matthews Band ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne R Fiori Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 1997 15:31:21 -0800 (PST) To: rasmol@noc1.oit.umass.edu On a tangent of this 2D/3D discussion. Is there a program out there that will take a pdb (or other common) format file and 'grow' hydrogens onto the structure?? -- ======================================================================== | Wayne R Fiori | e-mail: fiori@cmgm.stanford.edu | | Biochemistry Dept. | Phone: (415)723-6902 [Lab] | | Beckman Center, Stanford | (415)723-6161 [message] | | Stanford, CA 94305-5307 _________|_________ (415)723-6783 [fax] | ======================================================================== "Re: 2D and 3D images with Chime" (Feb 12, 3:31pm) References: <199702122331.PAA18329@cmgm.Stanford.EDU> ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew Dalke" Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 1997 17:51:52 -0600 To: rasmol@noc1.oit.umass.edu Wayne R. Fiori asked: > On a tangent of this 2D/3D discussion. Is there a program out there that > will take a pdb (or other common) format file and 'grow' hydrogens onto the > structure?? Babel, mentioned in Tim Bender's email can do this. As he said, Babel is at ftp.joplin.biosci.arizona.edu, and it is free. XPLOR can also do this, but it costs money. xplor.csb.yale.edu, if I recall. Andrew Dalke dalke@ks.uiuc.edu ++++------+------+------+------+------+------+------+------+------+------+ From: b_duke@lacebark.ntu.edu.au Subject: Re: 2D and 3D images with Chime Date: Thu, 13 Feb 1997 09:42:14 +1000 (EET) To: rasmol@noc1.oit.umass.edu > > Wayne R. Fiori asked: > > On a tangent of this 2D/3D discussion. Is there a program out there that > > will take a pdb (or other common) format file and 'grow' hydrogens onto the > > structure?? > > Babel, mentioned in Tim Bender's email can do this. As he said, > Babel is at ftp.joplin.biosci.arizona.edu, and it is free. This did not work for me. I found it at joplin.biosci.arizona.edu in /pub/Babel. For unix it looks as if 1.6 is the latest version. There are older unix versions there and PC and Mac versions. Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89410460 e-mail: b_duke@lacebark.ntu.edu.au WWW http://lacebark.ntu.edu.au/chemistry References: <9702122342.AA14252@lacebark.ntu.edu.au> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 1997 16:32:14 -0800 To: rasmol@noc1.oit.umass.edu > > This did not work for me. I found it at joplin.biosci.arizona.edu > in /pub/Babel. For unix it looks as if 1.6 is the latest version. > There are older unix versions there and PC and Mac versions. Now that you mention it, I seem to remember having some problems there - If I recall correctly, the way I solved it was to not use the babel command line, but use the menu (babel -m). If this still doesn't work, try converting the pdb file into an xyz and then convert that into a mol file. Keep trying....babel really does work......... References: ; from "Fergus Doherty" at Feb 12, 97 1:50 pm ++++------+------+------+------+------+------+------+------+------+------+ From: Tom Dearie Subject: Babel - trouble finding it Date: Thu, 13 Feb 97 20:42 EST To: rasmol@noc1.oit.umass.edu Cc: tbender@ccs.carleton.ca Tim- What program did you use to access ftp.joplin.biosci.arizona.edu? I tried netscape and fetch, but was told by both that there was no host by that name. Thanks in advance. TGD References: <199702122310.XAA21556@rideau> ; from "Fergus Doherty" at Feb 12, 97 1:50 pm ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Re: Babel - trouble finding it Date: Fri, 14 Feb 1997 09:41:14 +0000 To: rasmol@noc1.oit.umass.edu >Tim- >What program did you use to access ftp.joplin.biosci.arizona.edu? >I tried netscape and fetch, but was told by both that there was no host by >that name. > >Thanks in advance. > >TGD Leave out the ftp., just joplin.biosci.arizona.edu worked for me 9same problem as you to start with). Fergus _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html ++++------+------+------+------+------+------+------+------+------+------+ From: Mr AJ Pemberton Subject: Re: Babel - trouble finding it Date: Fri, 14 Feb 1997 11:10:47 +0000 (GMT) To: rasmol@noc1.oit.umass.edu On Thu, 13 Feb 1997, Tom Dearie wrote: > Tim- > What program did you use to access ftp.joplin.biosci.arizona.edu? > I tried netscape and fetch, but was told by both that there was no host by > that name. > > Thanks in advance. > > TGD > > > The babel ftp site is: joplin.biosci.arizona.edu not ftp.joplin.biosci.arizona.edu Tony P. ********************************************************************** Mr. A.J.Pemberton c/o Dept. Rheumatology, Tel: +121-414-3388 Medical School, Fax: +121-414-6794 The University of Birmingham, Email: A.J.Pemberton@bham.ac.uk Birmingham B15 2TT. www: http://sgisw.bham.ac.uk/~pemberaj/ U.K. ********************************************************************** References: ++++------+------+------+------+------+------+------+------+------+------+ From: Bernhard Vogler Subject: Re: Babel - trouble finding it Date: Fri, 14 Feb 1997 16:16:20 +0100 To: rasmol@noc1.oit.umass.edu At 11:10 14.02.97 +0000, you wrote: >On Thu, 13 Feb 1997, Tom Dearie wrote: > >> Tim- >> What program did you use to access ftp.joplin.biosci.arizona.edu? >> I tried netscape and fetch, but was told by both that there was no host by >> that name. >> >> Thanks in advance. >> >> TGD >> >> >> > >The babel ftp site is: > >joplin.biosci.arizona.edu > >not > >ftp.joplin.biosci.arizona.edu > >Tony P. > >********************************************************************** >Mr. A.J.Pemberton >c/o Dept. Rheumatology, Tel: +121-414-3388 >Medical School, Fax: +121-414-6794 >The University of Birmingham, Email: A.J.Pemberton@bham.ac.uk >Birmingham B15 2TT. www: http://sgisw.bham.ac.uk/~pemberaj/ >U.K. >********************************************************************** > > > Use Netscape : adress ftp://joplin.biosci.arizona.edu or an ftp-client: ftp to joplin.biosci.arizona.edu than anonymous ( login) and mailadress (passwd) Regards B. V. ------------------------------------------------ Bernhard Vogler Institut fuer Chemie Universitaet Hohenheim Garbenstrasse 30 70599 Stuttgart Tel.: (49)711 - 459 - 2944 - 2963 (NMR) - 3908 (Computer Raum) FAX:(49)711 - 459 - 2951 e-mail: chemvogl@uni-hohenheim.de ------------------------------------------------ ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Gryko Subject: Colors and bonds in rasmol Date: Fri, 14 Feb 1997 08:56:07 -0700 To: "'rasmol@lists.umass.edu'" Several days ago I asked how to select color for atoms like iron, zinc, and other metals and how to force rasmol to draw bonds between metals. Any suggestions? Thanks, J. Gryko College of Eastern Utah > ++++------+------+------+------+------+------+------+------+------+------+ From: Gregory Flack Subject: Re: Colors and bonds in rasmol Date: Fri, 14 Feb 1997 10:05:02 -0700 (MST) To: rasmol@noc1.oit.umass.edu One can color specific elements by using the select and color commands. For example: select iron color red Don't forget to use the 'spacefill' command to see the atoms afterwards because metals are typically a point in space and if they are not connected a wireframe or similar symbology won't display them. I am unaware of a command for drawing a line between atoms when there is no instruction in the molecule file for this. Although I haven't taken the time to explore the architecture of the file, there is bonding information at the end of a PDB file and that can be edited to give a bond you desire. I expect that other file types can be edited in this way also. I have forgotten the exact nature of your inquiry days back, but I hope this helps. -Greg ------------------------------------------- Gregory Flack gsflack@holly.colostate.edu undergraduate - Department of Microbiology Colorado State University, Fort Collins, CO ------------------------------------------- On Fri, 14 Feb 1997, Jan Gryko wrote: > > Several days ago I asked how to select color for atoms like iron, zinc, > and other metals and how to force rasmol to draw bonds between metals. > Any suggestions? Thanks, > > J. Gryko > College of Eastern Utah > > > > ++++------+------+------+------+------+------+------+------+------+------+ From: Chris Milne Subject: Re: Colors and bonds in rasmol Date: Fri, 14 Feb 97 12:12:26 EST To: rasmol@noc1.oit.umass.edu under colour there's a user defined choice (for windows system). there's another option under the command-line interface. just use the help file to figure it out ! as for forcing bonds, you can try converting it to a mol file then opening it in chem draw/web and drawing the bonds in then re-opening it in RasMol. ----------------------------------------------------------------------- Chris Milne Carleton University "But then came the day I climbed out of these safe limbs Ventured away Walking tall, head high up, and singing I went to the city Car horns, corners and the gritty Now I am the proudest monkey you've ever seen" - Dave Matthews Band References: <199702122310.XAA21556@rideau> ; from "Fergus Doherty" at Feb 12, 97 1:50 pm ++++------+------+------+------+------+------+------+------+------+------+ From: Tom Dearie Subject: Re: Babel - trouble finding it Date: Sun, 16 Feb 97 14:20 EST To: rasmol@noc1.oit.umass.edu Thanks to all for help in getting Babel. One question: I downloaded version 1.03 for Mac, posted in 1994. Does anyone know if there's a more recent version? Tom Dearie BioLogic Scientific Communications, Toronto, Canada. ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: chime web pages Date: Mon, 24 Feb 1997 10:08:10 -0800 To: rasmol@noc1.oit.umass.edu Hi-sorry if this already asked...uploaded new chime-capable web page to my server. When I try to access it, it trys to open rasmol instead of chime. My browser (netscape) works normally on chime sites on other servers - is this a mime problem at my server or something at my end? Thank you kindly.............. ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: mime types Date: Mon, 24 Feb 1997 10:37:33 -0800 To: rasmol@noc1.oit.umass.edu Sorry to bother everyone - clear case of RTFM. Answered my own question at http://www.mdli.com/chemscape/chime/chimehelp.html#Install5. Thank you for your patience. types] ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: chime web pages [Configuring web server for Chemical MIME Date: Mon, 24 Feb 1997 10:30:28 -0800 To: skg@asis.com, rasmol@noc1.oit.umass.edu At 10:08 AM 2/24/97 -0800, you wrote: >Hi-sorry if this already asked...uploaded new chime-capable web page >to my server. When I try to access it, it trys to open rasmol instead of >chime. My browser (netscape) works normally on chime sites on other >servers - is this a mime problem at my server or something at my end? >Thank you kindly.............. > You must configure your web server to serve the MIME types of the chemical files. There is information in the Chime FAQ that tells how to do this for several web servers: http://www.mdli.com/chemscape/chime/chimehelp.html#Install5 -tim ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: 2D and 3D images with Chime Date: Mon, 24 Feb 1997 17:26:33 -0800 To: rasmol@noc1.oit.umass.edu At 05:50 AM 2/12/97 -0800, Fergus Doherty wrote: >I know Chime can display .mol files as 2D representations of molecules, and >as "3D". But if I create a 2D mol file with ISIDraw this doesn't contain >3D information and the file in "3D" viewed with Chime is flat. A PDB file >viewed in Chime on the other hand can only be viewed in 3D. > >What I want to be able to do is use Chime to load one file (of a small >molecule, say cAMP) and view this in 2D, and switch to "real" 3D with the >Chime menu. We hope to have 3D 'automatic' coordinate generation for 2D structures in a future version of Chime. The Chemscape/Chime team at MDL is extremely fortunate that Michael Hartshorn has joined our team. He will be working with Roger Sayle at GlaxoWellcome on exciting new extensions to the Rasmol/Chime 'platform'. Among these *possible* features is a very fast 3D coordinate generator Michael has developed (Michael's algorithm also sprouts hydrogens) BTW, there is a bug in the Chime 1.0 release which prevents you from entering 2D mode from 3D mode. This will be fixed in an upcoming release. -tim >Is this possible, and if so how would I generate the necessary file? > >If not, is there another way to do it (load mol or pdb files with an >embedded script and button)? > >Finally, how can I generate pdb files from 2D representations of simple >molecules - would I need something lke Chem3D to do this? > >TIA > >Fergus > > >_____________________________________________________________________ >Fergus Doherty PhD >Dept. Biochemistry, >University Medical School, >Queen's Medical Centre, >Nottingham NG7 2UH > >e-mail: Fergus.Doherty@nottingham.ac.uk >Tel: 0115 970 9366 >FAX: 0115 942 2225 >URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html > > > > References: <3.0.32.19970224172251.00c00d98@mind.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: 2D and 3D images with Chime Date: Mon, 24 Feb 1997 21:04:54 -0800 To: rasmol@noc1.oit.umass.edu . He will be working with Roger Sayle > at GlaxoWellcome on exciting new extensions to the Rasmol/Chime 'platform'. > Among these *possible* features is a very fast 3D coordinate generator > Michael has developed (Michael's algorithm also sprouts hydrogens) > > BTW, there is a bug in the Chime 1.0 release which prevents you > from entering 2D mode from 3D mode. This will be fixed in an > upcoming release. > > -tim > Awesome! Thanks again....I see what you mean about 2D from 3D - but all you have to do is use a mol file & you can have both, so it's really no problem.....Cheers... , , , ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: RE: Chime and MS IE 3.01 under Win95 Date: Tue, 25 Feb 1997 20:38:48 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: , , Download Netscape Navigator 3.01 from www.netscape.com. It is free for academic users. -Eric In message Mon, 10 Feb 1997 19:14:52 +0000, "Sergey A. Vasil'ev" writes: > Hi, > > I try to install Chime 1.0 on my computer (Windows95 and IE 3.01) but > it says that Chime doesn't work without Netscape Navigator. > > What can I do? > > > Sergey Vasil'ev,M.Sc. > > Computer Modeling Group, > Institute of Agricultural BioTechnology, > 42 Timiryazevskaya st., > Moscow, 127550, Russia > > tel. 7(095)211-0509 > fax. 7(095)216-4777 > e.mail vasil@iabunix.iab.ac.ru > vasil@agrobio.msk.su > /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Babel: history, websites, hydrogens. Date: Wed, 26 Feb 1997 14:37:52 -0500 (EST) To: Cc: rick_hallick@tikal.biosci.arizona.edu Rick's message below was rejected by listproc for technical reasons and then delayed due to my being out of town. Here it is at last. ++++------+------+------+------+------+------+------+------+------+------+ From: Rick Hallick Subject: Re: 2D and 3D images with C Date: Fri, 14 Feb 1997 To: rasmol@noc1.oit.umass.edu Babel was written by Pat Walters and Matt Stahl, doctoral students at the University of Arizona Department of Chemistry in the lab of Dan Dolata. We have hosted the archives on one of our servers at joplin.biosci.arizona.edu for many years. Pat, Matt, and Don have all left the University of Arizona. However there is still a legacy web site for Babel at: http://mercury.aichem.arizona.edu/babel.html We continue to mirror the archives at joplin.biosci.arizona.edu, but we may transfer the mirror site to http://www.blc.arizona.edu. Meanwhile, Matt and Pat are now in the private sector, Dan has moved to Ohio, and the current archives have moved with him to the following address: ftp://ccl.osc.edu/pub/chemistry/software/MAC/babel/ Babel is a useful program for adding hydrogens to PDB format files, but it does make mistakes in some situations, such as modified bases in tRNAs. Another disadvantage is that all of the information except atom number and x, y, z coordinates are lost when Babel writes new files. RasMol users might also be interested in learning more about MacMolecule2 and PCMolecule2 molecular graphics programs: http://www.blc.arizona.edu/linus/linus.html Richard Hallick Professor of Biochemsitry University of Arizona hallick@arizona.edu http://www.blc.arizona.edu/rick/ [Forwarded by: /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: GRIFFITHSJ@rsc.org Subject: Chime help Date: Thu, 27 Feb 1997 17:42 +0000 (GMT) To: rasmol@noc1.oit.umass.edu Dear all As part of the CLIC Consortium (see URL below), I receive various structure files from authors who wish these included with the enhanced web version of their ChemComm publication. For viewing purposes, we rely on the Chime plugin for Netscape Generally, these structure files are either PDB files or XYZ files. If the author wishes a specific "initial" view, then I've achieved this by using either using in-line script files or CSML files (I've not ventured into blending JavaScript with Rasmol script files yet). Often, I receive structure files of inorganic compounds where the organometallic bonds don't appear (I believe this is due to bond lengths exceeding those expected by Chime). So far, I've only had to show spacefilling models and by setting the radii of the spacefill atoms I can make reasonable representations. However, to force Chime to draw bonds in (say) wireframe mode, I believe I'm correct in saying that the structure file needs some connecting information (CONECT ...). However, there are various points I'm not sure about here, such as whether this is only available for PDB files and not XYZ files etc, what is the correct syntax etc. Also, I often get given so-called PDB and XYZ files that don't parse correctly with Chime (or generic programs) and I have to hack these manually to get them to display. I guess I could answer these problems myself if I knew the specifications for both file formats - could anybody point me to where I could find these (and other ?) specifications? My second question also involves inorganic compounds. Is there any way to show a crystal structure in the polyhedra format? Any help would be much appreciated .. regards Griff ---------- Dr Jonathan Griffiths 1) The CLIC Consortium - http://chemcomm.clic.ac.uk/ 2) NewMedia, The Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, United Kingdom Tel/Fax: +44 (0)1223 432136/420247, http://chemistry.rsc.org/rsc/ ---------- ++++------+------+------+------+------+------+------+------+------+------+ From: LEVY SAM Subject: Rasmol to Molscript Problems Date: Thu, 27 Feb 1997 14:26:15 -0700 (MST) To: rasmol@noc1.oit.umass.edu Cc: levy@spot.colorado.edu I have been using Rasmol(2.6) to orientate molecules on a Unix workstation employing stereo mode and then output the viewing transformation into a Molscript file using the Rasmol command write molscript (output_filename) When I execute Molscript using the file outputted by Rasmol as Molscript input, the resulting postscript image depicts a 'mirror' image of the original Rasmol view. As far as I can tell, the z-coordinate is somehow interpretted as -z. Has anyone experienced this behavior and (most importantly) found a fix. Any help would be appreciated. ------------------------------------------------------------------------------- Samuel Levy, Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, 80309-0347, USA Tel:+1 303 492 8893 Fax:+1 303 492 7744 Email: levy@spot.colorado.edu ------------------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Mr AJ Pemberton Subject: Re: Chime help Date: Fri, 28 Feb 1997 09:24:29 +0000 (GMT) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu On Thu, 27 Feb 1997 GRIFFITHSJ@rsc.org wrote: > > Dear all > > As part of the CLIC Consortium (see URL below), I receive various > structure files from authors who wish these included with the enhanced > web version of their ChemComm publication. For viewing purposes, we > rely on the Chime plugin for Netscape > > Generally, these structure files are either PDB files or XYZ files. > If the author wishes a specific "initial" view, then I've achieved > this by using either using in-line script files or CSML files (I've > not ventured into blending JavaScript with Rasmol script files yet). > > Often, I receive structure files of inorganic compounds where the > organometallic bonds don't appear (I believe this is due to bond > lengths exceeding those expected by Chime). So far, I've only had to > show spacefilling models and by setting the radii of the spacefill > atoms I can make reasonable representations. However, to force Chime > to draw bonds in (say) wireframe mode, I believe I'm correct in saying > that the structure file needs some connecting information (CONECT > ...). However, there are various points I'm not sure about here, such > as whether this is only available for PDB files and not XYZ files etc, > what is the correct syntax etc. Also, I often get given so-called PDB > and XYZ files that don't parse correctly with Chime (or generic > programs) and I have to hack these manually to get them to display. I > guess I could answer these problems myself if I knew the > specifications for both file formats - could anybody point me to where > I could find these (and other ?) specifications? see http://www2.ebi.ac.uk/pdb/Format.doc/Contents_Guide_21.html for PDB format I am not sure about XYZ! Tony P. ********************************************************************** Mr. A.J.Pemberton c/o Dept. Rheumatology, Tel: +121-414-3388 Medical School, Fax: +121-414-6794 The University of Birmingham, Email: A.J.Pemberton@bham.ac.uk Birmingham B15 2TT. www: http://sgisw.bham.ac.uk/~pemberaj/ U.K. ********************************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: GRIFFITHSJ@rsc.org Subject: PDB file and groups Date: Fri, 28 Feb 1997 17:11 +0000 (GMT) To: rasmol@noc1.oit.umass.edu Dear All I have a PDB file ( > 900 atoms) that I wish to display with the colour scheme specified by group. Unfortunately, when the file was generated, no group information was added. Using Chem3D I can add the group information, but I can't save this group information in any file format other than the native Chem3D file; does anyone know of any software (preferably freeware that runs on Windows 3.11) that would allow me to achieve my aim? (I do have limited access to a PC running 95 and NT 4.0) Many thanks in advance Griff ---------- Dr Jonathan Griffiths 1) The CLIC Consortium - http://chemcomm.clic.ac.uk/ 2) NewMedia, The Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, United Kingdom Tel/Fax: +44 (0)1223 432136/420247, http://chemistry.rsc.org/rsc/ ---------- ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Pre-arrange RasMol windows in Win95 Date: Fri, 28 Feb 1997 19:47:47 -0500 (EST) To: Not long ago, I mentioned here the shareware Freezeframe which makes RasMol's windows start up in the same positions and sizes as when it was last closed. But Freezeframe works only for Windows 3.1. Rod Levine (NIH) pointed out to me a solution for Windows 95, Deskey from Softarts, www.spiresoft.com. The shareware version runs for 1 hr at a time for 30 days. Registration is $15. When you run Deskey's SETUP.EXE, nothing seems to happen. However, at the right end of the Taskbar (the bar with Start on it), you will now see a gold key. Click on this for Deskey's menu. Start RasMol and arrange the graphics window as you want it. Now select Window Placements on Deskey's menu, Add, Capture from window, and OK the Add Window Placement Dialog (no further changes are necessary; be sure to leave the Auto-apply option checked). Now arrange the RasMol Command Line window and do the same sequence to add a window placement in Deskey. Close RasMol, restart it, and voila! Your window arrangement is automatically restored for both windows. If you have multiple icons for multiple RasMol scripts, you do not have to add window placements for each icon. Deskey recognizes RasMol as such regardless of which icon you use to start it. Enjoy! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Andrea Bernini Subject: Hbonds in pdb. Date: Mon, 3 Mar 1997 14:30:41 +0100 (MET) To: Rasmol mailing list I know Rasmol calculates H-bonds, but does exist a way to put hbonds directly in pdb records? Thanks in advance. ++++------+------+------+------+------+------+------+------+------+------+ From: "Francis M.J. Hsieh" Subject: Re: Hbonds in pdb. Date: Tue, 4 Mar 1997 02:49:45 +0800 (WST) To: rasmol@noc1.oit.umass.edu In the article, Andrea Bernini wrote: > I know Rasmol calculates H-bonds, but does exist a way to put > hbonds directly in pdb records? I think the standard pdb format doesn't content hbond information. And the pdb format is not only for RasMol. :p -- Francis M.J. Hsieh | email: mjhsieh@life.nthu.edu.tw Graduate student at Dept. of Life | Homepage: Science, National TsingHua Univ., | http://life.nthu.edu.tw/~mjhsieh/ Taiwan. | TEL: +886 3 5715131 ext 3482 ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: Re: Hbonds in the PDB Date: Mon, 3 Mar 1997 14:52:23 -0500 To: rasmol@noc1.oit.umass.edu Just to set the record straigt, PDB's Contents Guide (http://www.pdb.bnl.gov/Format.doc/Format_Home.html) specifies the format for hydrogen bonds. The HYDBND record is optional, but sometimes is supplied in the submission to PDB. I believe that these records are handmade by the authors, but perhaps someone knows of a program which writes them out. Regards, Nancy Excerpt from the PDB Content Guide: HYDBND Overview The HYDBND records specify hydrogen bonds in the entry. Record Format COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "HYDBND" 13 - 16 Atom name1 Atom name. 17 Character altLoc1 Alternate location indicator. 18 - 20 Residue name resName1 Residue name. 22 Character Chain1 Chain identifier. 23 - 27 Integer resSeq1 Residue sequence number. 28 AChar ICode1 Insertion code. 30 - 33 Atom nameH Hydrogen atom name. 34 Character altLocH Alternate location indicator. 36 Character ChainH Chain identifier. 37 - 41 Integer resSeqH Residue sequence number. 42 AChar iCodeH Insertion code. 44 - 47 Atom name2 Atom name. 48 Character altLoc2 Alternate location indicator. 49 - 51 Residue name resName2 Residue name. 53 Character chainID2 Chain identifier. 54 - 58 Integer resSeq2 Residue sequence number. 59 AChar iCode2 Insertion code. 60 - 65 SymOP sym1 Symmetry operator for 1st non-hydrogen atom. 67 - 72 SymOP sym2 Symmetry operator for 2nd non-hydrogen atom. Details * The hydrogen bonds listed normally are those supplied by the depositor. * The atoms forming the hydrogen bond are listed on the HYDBND record. * Each record has place for three atom specifications. * Columns 13 - 28 and 44 - 59 are for the atoms associated with the hydrogen atom of the hydrogen bond. * If the coordinates of the hydrogen atom itself are presented in the entry, that atom is specified in columns 30 - 42. * For nucleic acids, Watson-Crick hydrogen bonds between bases may be listed, but this is optional. * sym1 and sym2 are given as blank when the identity operator (and no cell translation) is to be applied to the atom. For hydrogen atoms use the symmetry operator of the heavy atom to which it is bonded. Verification/Validation/Value Authority Control The distance between the atoms listed must be consistent with the bonding. Relationships to Other Record Types CONECT records are generated consistent with the bond type. If symmetry operators are given to generate one of the residues involved in the hydrogen bond, REMARK200 defines the symmetry transformation. Example 1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012 HYDBND N LEU 10 AO3* NDP 501 HYDBND NH2 ARG 111 OD1 ASP 149 1555 -- _______________________________________________________________________ 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: Wayne R Fiori Subject: Re: Hbonds in pdb. Date: Mon, 3 Mar 1997 11:59:55 -0800 (PST) To: rasmol@noc1.oit.umass.edu > > In the article, Andrea Bernini wrote: > > I know Rasmol calculates H-bonds, but does exist a way to put > > hbonds directly in pdb records? > > I think the standard pdb format doesn't content hbond information. > And the pdb format is not only for RasMol. :p > The CONECT record can specify hydrogen bonding. Unfortunately, I don't remember the exact manner (columns and numbers) needed to do this. Take a look at Brookhaven's on line docs. It should be there. =Wayne ++++------+------+------+------+------+------+------+------+------+------+ From: tpthoms Subject: Rasmol: Limitations and compilation Date: Mon, 03 Mar 1997 18:18:52 -0500 To: rasmol@noc1.oit.umass.edu Hi! I'm a student at U.C. Irvine, and while using your wonderful software, I ran into an error while trying to display a molecule we are attempting to synthesize: Database error:Too many new atom types! This error occurs in both the windows and macintosh version of your software. What does it mean? Secondly, I am trying to compile Rasmol for XFree86/OS2 and I received the following message: [D:\tar\rasmol2]make gcc -m486 -O2 -fno-strength-reduce -D__ST_MT_ERRNO -Zmtd -Zsysv-signals -Id:/ XFree86/include -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/XFree86/lib/rasm ol/\" -DEIGHTBIT -c rasmol.c -o rasmol.o rasmol.c: In function `InitTerminal': rasmol.c:264: sizeof applied to an incomplete type rasmol.c: In function `FetchCharacter': rasmol.c:337: invalid use of undefined type `struct fd_set' rasmol.c:338: invalid use of undefined type `struct fd_set' rasmol.c:350: invalid use of undefined type `struct fd_set' rasmol.c: At top level: rasmol.c:110: storage size of `WaitSet' isn't known X11MAKE.EXE: *** [rasmol.o] Error 1 Is their some compiler switch that I missed? Any help you can give would be greatly appreciated. Thanks Travis Thoms tpthoms@mail.fia.net ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Rasmol: Limitations and compilation Date: Wed, 5 Mar 1997 15:22:25 +0000 (GMT) To: tpthoms Cc: rasmol@noc1.oit.umass.edu Hi Travis, > I ran into an error while trying to display a molecule we are > attempting to synthesize: > "Database error:Too many new atom types!" > This error occurs in both the windows and macintosh version of your > software. What does it mean? Thanks very much for your e-mail. This problem is caused when RasMol attempts to define new indices for the atom names defined in the input co-ordinate file. Normally in a PDB or similar file atoms are given unique names within a residue such as " CA " or " O1P". RasMol uses indices into an array rather than a string for each of these to reduce the overhead in storing and comparing them. The above error is caused when RasMol discovers too many new names in a file. The current limit is 256 which is considered sufficient as Brookhaven only needs 67 for all standard protein and nucleic acid atoms. The probable cause of this error is either that the column formating in your co-ordinate file is wrong or you are attempting to name atoms as "C1", "C2", "C3", etc... > Secondly, I am trying to compile Rasmol for XFree86/OS2 and I received > the following message: > > [D:\tar\rasmol2]make > gcc -m486 -O2 -fno-strength-reduce -D__ST_MT_ERRNO -Zmtd > -Zsysv-signals -Id:/ > XFree86/include -DFUNCPROTO=15 -DNARROWPROTO > -DRASMOLDIR=\"/XFree86/lib/rasm > ol/\" -DEIGHTBIT -c rasmol.c -o rasmol.o > rasmol.c: In function `InitTerminal': > rasmol.c:264: sizeof applied to an incomplete type > rasmol.c: In function `FetchCharacter': > rasmol.c:337: invalid use of undefined type `struct fd_set' > rasmol.c:338: invalid use of undefined type `struct fd_set' > rasmol.c:350: invalid use of undefined type `struct fd_set' > rasmol.c: At top level: > rasmol.c:110: storage size of `WaitSet' isn't known > X11MAKE.EXE: *** [rasmol.o] Error 1 It sounds as though the UNIX structure "struct fd_set" is not being defined by any of the OS2 header files. This is used by RasMol as an argument to the UNIX select(2) system call to multiplex stdin and X Windows events. Fortunately, this dependency can be removed from RasMol by commenting out the line "#define TERMIOS" in the "rasmol.h" header file. This will instruct RasMol not to use "select" or "struct fd_set" but will mean that you can no longer type commands into the controlling "xterm" window. However, you can still type into the main RasMol graphics window (when it has input focus). I hope this helps. Please let me know how you get on. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: BABEL Home Page Date: Wed, 5 Mar 1997 13:34:40 -0500 (EST) To: ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Debord Subject: BABEL Home Page Date: Tue, 4 Mar 1997 13:03:07 -0500 To: Rasmol List [This got rejected by listproc over a technicality so I'm forwarding it. -Eric] Dear All, A home page is now available for BABEL, a program to convert between different chemical file formats. Its URL is: http://mercury.aichem.arizona.edu/babel.html It is possible to download BABEL and to register it on-line. I hope you will find this information useful. Sincerely, Jean Debord Faculte de Medecine, Limoges, France /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Hbonds in the PDB Date: Tue, 11 Mar 1997 19:34:02 +0000 (GMT) To: rasmol@noc1.oit.umass.edu Dear RasMolians, > Just to set the record straigt, PDB's Contents Guide > (http://www.pdb.bnl.gov/Format.doc/Format_Home.html) specifies the > format for for hydrogen bonds. The HYDBND record is optional, but > sometimes is supplied in the submission to PDB. I believe that these > records are handmade by the authors, but perhaps someone knows of a > program which writes them out. Unfortunately RasMol currently does not support specification of hydrogen bonds by either CONECT or HYDBND records. HYDBND and many other version 2.x features will hopefully be supported in the next release of RasMol. Alas Wavefunction's Spartan software places covalent bonding information in the hydrogen bond fields of the CONECT record (v1.0). As there seem to be more PDB files generated by Spartan and MacSpartan than PDB files containing explicit hydrogen bonds it was decided to support the former. Luckily, the new HYDBND record has helped resolve the issue. It is possible to specify hydrogen bonds to RasMol in Alchemy file format using the bond type "HYDROGEN". However this conversion will loose all of the macromolecular information that is in a PDB file. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Group color scheme: RasMol manual revised Date: Sun, 16 Mar 1997 11:59:37 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: ras32425@ggr.co.uk, tim@mind.net I have made a minor revision to the on-line (html) RasMol manual (the only version which is up to date, http://www.umass.edu/microbio/rasmol/distrib/rasman.htm). The discussion of the group color scheme omitted mention of the need for a 'set hetero off' command to exclude e.g. water from the spectral range, thereby applying the full range from blue to red to the protein chain. The manual also appeared to me to have the colors reversed for protein, e.g. the N terminus is blue, and the C terminus red, so I corrected that. (Thanks to Roger Sayle for explaining about this effect of 'set hetero off' in an email message to this list, 3/14/96. Sorry that it took me a year and 2 days to integrate this info into the manual!) ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Multiple molecules Date: Mon, 17 Mar 1997 17:36:05 -0500 (EST) To: Dear Rasmolites & Chimeleans: I thought the following ideas from Roger Sayle (in response to my comments on Marcey's illustration of a process) would be of interest. Unlike Marco Molinaro's Berkeley-enhanced RasMol, the ideas below (using Sayle's RasMol without modification) do not allow independent movement of the separate molecules. However, they do facilitate the control of the display or hiding of separate molecules. -Eric Martz ------------------------------ Fri, 14 Mar 1997 From: Sayle Dr R A Hi Eric, [Eric wrote to Roger:] > David Marcey recently put out a chime tutorial on topoisomerase. [www.kenyon.edu/depts/bmb/chime.htm] > He modeled PDB files for 6 different stages in the reaction: a single > stranded DNA is covalently bound to a tyrosine, the molecule cleaves the > SS-DNA, then opens and 'grabs' a double stranded DNA, then closes, > religates the SS-DNA, reopens and releases the DS-DNA. Such a process > would be much easier to comprehend in Molinaro's Berkeley-enhanced rasmol [which would allow moving domains independently of each other] > than with snapshots, but I'm shy of scripting with it in Windows because > when you do a zap from a script file, it hangs (may not do this on the Mac). [Roger Sayle replies:] As I keep insisting RasMol is capable of handling multiple molecules, however all the molecules of interest must be stored in a single file. For example, if you just concatenate Brookhaven PDB files together RasMol will treat the END records in the file to deliniate different molecules. A much better way to organise an animation like this is to use the MODEL and ENDM records in a PDB file, or different chain identifiers. In this way, a RasMol (or Chime) script can be used to turn on or off the displays of chains or models independently. Locally, short scripts are used to cycle through a number of protein inhibitors displayed within the active site. One chain contains all of the protein atoms that don't move and a series of other chains contain the active site side chains and inhibitors. These are then turned on and off with the single click of a button in Netscape or with a single RasMol script without containing a "zap". Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: baucom@gorby.UCSC.EDU (Albion Baucom) Subject: StartSpin As A Script Command Date: Tue, 18 Mar 1997 09:55:31 -0800 To: rasmol@noc1.oit.umass.edu I was attempting to place a startspin button on a web page with an embeded chime model and could not find a Rasmol script command to start rotation of a model. The Chime menu has a "Rotation" command which leads me to believe that there must be some kind of command to start the model spinning, but the only command I have found is a property of the model embed tag and it only lets you start the model spinning when it is loaded. I would ultimately like to have a button on the page that would toggle spinning on and off, as well as have a speed control. If there is currently no "spin" script command, I could see it being an important addition to a future version of chime. If anyone knows of a spin script command, or a javascript function that uses "rotation" to spine a molecule, I would greatly appreciate their suggestions or recommendations. Thanks in advance. Albion E. Baucom baucom@gorby.ucsc.edu UC Santa Cruz 241B Sinsheimer Labs Santa Cruz, CA 95064 (408) 920-1616 ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Miller Subject: Re: StartSpin As A Script Command Date: Wed, 19 Mar 1997 10:41:03 -0800 To: baucom@gorby.ucsc.edu Cc: rasmol@noc1.oit.umass.edu, chime-feedback@mdli.com Hello Albion, There are currently two ways to set up buttons that can start/stop rotation of a Chime structure. Both have some advantages/drawbacks. 1) Put the structure in a separate frame and use an HTML button to (re)load the structure frame: This approach does require you to put the structure in a separate frame and when a frame is reloaded, the user will loose any modifications made to the display. You could make the onClick function smarter so it can act as a toggle. 2) Using 'script="move 360000 0 0 0 0 0 0 0 500 15 1"' or something of this nature instead of 'spinx=10 startstpin=yes' in your tag. The move command is actually designed to perform discreet rotations over a finite time span but, when given large input values, will make the structure rotate for a long time. You can create two Chime buttons, one with script move 360000 0 0 0 0 0 0 0 500 15 1 and the other with script interrupt to stop the rotation. This approach will let you keep the structure in the same frame as the rest of the page and will preserve what the user has done to the display (e.g., changing to spacefilling view) but 'move' can consume more system resources than other commands. We're looking at a more efficient approach for the future. Mitch At 09:55 AM 3/18/97 -0800, Albion Baucom wrote: > >I was attempting to place a startspin button on a >web page with an embeded chime model and could not >find a Rasmol script command to start rotation of a >model. The Chime menu has a "Rotation" command which >leads me to believe that there must be some kind of >command to start the model spinning, but the only >command I have found is a property of the model >embed tag and it only lets you start the model spinning >when it is loaded. > I would ultimately like to have a button on the >page that would toggle spinning on and off, as well as >have a speed control. If there is currently no "spin" >script command, I could see it being an important addition >to a future version of chime. > >If anyone knows of a spin script command, or a javascript >function that uses "rotation" to spine a molecule, I would >greatly appreciate their suggestions or recommendations. > >Thanks in advance. > > >Albion E. Baucom > > >UC Santa Cruz >241B Sinsheimer Labs >Santa Cruz, CA 95064 >(408) 920-1616 > Mitchell Miller MDL Information Systems, Inc. (801) 569-1390 VoiceMail (800)955-0051 ext. 2163 mitch@mdli.com ctheurer@bio.umass.edu, rasmol@noc1.oit.umass.edu, ahuja@centaurus.cs.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: RE: Q on Rasmol coloring atoms Date: Wed, 19 Mar 1997 21:04:25 +0000 (GMT) To: Eric Martz Cc: jacobs@pa.msu.edu, bscott@biochem.umass.edu, cfinlays@elux3.cs.umass.edu, Dear Don, > I do not believe you can color atoms differently from bonds, while > retaining half-and-half coloring of bonds. I have CC'd this to > Roger Sayle who can answer authoritatively, and also to the RasMol > Email list as your question and the answer may be of general interest. Eric is quite right that a bond can only be colored half-and-half if the two colours of that bond are the colours of the atoms at either end. I'm not sure if it was clear from the question, but it is possible to colour atoms and bonds completely independently. i.e. select all colour bonds red colour atoms yellow A thought has just struck me... It may be possible to achieve the same effect as you require by adding additional atoms at the end of the bonds with exactly the same co-ordinates. For example, if you wanted to draw a single bond between atoms A and B, you'd add two extra atoms C and D with exactly the same co-ordinates to the molecule file. Now instead of a single bond AB, RasMol will discover six AB,AC,AD,BC,BD and CD. All bonds can be turned off using "select all", "wireframe off", and only the bond CD displayed using "set bondmode and", "select C,D", "wireframe 20". Next all the atoms except A and B can be turned off, "select C,D", "spacefill off". Finally, atoms A, B, C and D may be displayed different colours. This results in a ball and stick like representation where the stick bond is half-and-half coloured but differently from the "spheres" at the ends. I'm sorry if this is hideously confusing. In practice you only need place one of two pseudo-atoms at the boundries of your "mechanical regions". I shall try and think of an way of adding half-and-half bond colouring to RasMol for the next release. A second thought has just struck me (what two in one day!)... The above scheme is simpler by just inserting a single atom E half way between A and B. Now there are three bonds AB,AE,BE. The AB bond can be turned off and AE and BE can be coloured independently using the "color bond" command. One possible advantage of this is that each half of the bond can even have a different cylindrical radius or be displayed as dashes. Sorry for such hacks. The answer is it can be done with a little effort. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 764918 X-Info: Ross Labs R&D NT-Mail Server ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Schenz Subject: Rasmol and Internet Explorer Date: Wed, 26 Mar 1997 12:55:18 -0500 To: rasmol@noc1.oit.umass.edu We want to distribute molecular structures over our web-intranet using Rasmol as a viewer within a browser. Netscape works fine. But, we have problems using Microsoft Internet Explorer(MIE). After clicking on the .pdb link, Rasmol loads but no molecule is displayed (black screen). We've tried this from the Web with the same results. If we right-click on the link, but save it to disk and then open the pdb file with Rasmol, everything works fine. It seems as though MIE is not passing the file name on to Rasmol. Has anyone else had this problem or know of a solution? Tim _____________________________________________________________________ Timothy W. Schenz, Ph.D. tschenz@sr-server.rossnutrition.com Abbott Labs/Ross Prod. Div. Voice (614)624-7024 Columbus, OH 43215 FAX: (614)624-3070 _____________________________________________________________________ References: <2.2.32.19970326175518.009861fc@sr-server.rossnutrition.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: Rasmol and Internet Explorer Date: Thu, 27 Mar 1997 01:46:22 +0100 To: rasmol@noc1.oit.umass.edu > Has anyone else had this problem or know of a solution? Well, not exactly the same but sometimes (depending on the location of the file in my folder-structure) I have similar problems, when I want to start a *.pdb-file by clicking on it (it is registered as Rasmol-datafile). Don=B4t know the reaso though.. -- = Bye, Marc Saric Visit http://www.rat.de/marc_saric/index.htm ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Summer Workshops (Northeastern US) Date: Mon, 31 Mar 1997 12:54:58 -0500 (EST) To: rasmol@noc1.oit.umass.edu ** Free Workshops on Molecular Visualization for Undergraduate Bioscience Teaching ** Amherst MA -- Summer, 1997-8 Understanding the three-dimensional structures of proteins, DNA, RNA, and their interactions is difficult from flat pictures, yet grasping structure is important to understanding function. Free software is now available which displays attention-grabbing 3D animated images of biological molecules in depth-cued spacefilling color. RasMol (http://www.umass.edu/microbio/rasmol), which works on Windows or Macs, encourages self-directed exploration. Chime (http://www.umass.edu/microbio/chime) allows annotated preset views of molecules to be delivered as web tutorials. Free, hands-on workshops will be held this summer at the University of Massachusetts in Amherst to prepare college faculty with no prior experience to use molecular visualization in their classes. Participants will travel to the Amherst campus on three separate days (two this summer, one the following summer), and are responsible for their own travel expenses (and therefore are expected primarily from the Northeastern USA). Overnight accomodations will be provided free to those needing them (based on distance traveled). Participants will be expected to incorporate molecular visualization into their teaching, and to mentor two faculty colleagues at their home institution. The workshops will be led by Eric Martz, a Professor in the Department of Microbiology. Martz has innovated molecular structure tutorials which are in use throughout the USA and in dozens of other countries. The web site he created (see above) was visited by 40,000 people in 1996. 1997 dates are June 17 and 30 (workshop A), or June 19 and July 2 (workshop B). Workshops A and B also meet for one day in late June 1998. To obtain more detailed information and a REGISTRATION FORM, visit http://www.umass.edu/microbio/rasmol/workshop.htm or FAX a request to 413-545-1578, or email a request to emartz@microbio.umass.edu. Supported by the National Science Foundation (Undergraduate Faculty Enhancement, Division of Undergraduate Education) and the University of Massachusetts. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol Other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/  ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RHP benefits from snow Date: Tue, 1 Apr 1997 21:35:54 -0500 (EST) To: rasmol@noc1.oit.umass.edu There was a great snow here last night, which closed the U of Mass for the day. That had a beneficial effect on the RasMol Home Page, to wit (copied from "What's New?"): 97/04/01: Henry Brzeski's new RasMol "movie" script on glucocorticoid/zinc finger binding to DNA has been linked. 97/04/01: A list of frequently asked questions, with answers, has been contributed by Roger Sayle. My apologies to Roger for taking far too long to find the time to put this very useful FAQ on the web site. 97/04/01: Babel, a web interface to Babel, MolView, and other links were added to the page on free software other than RasMol, which was also reorganized and better indexed. Now included is an amazing web form which allows you to submit a PDB to RasMol and get back a single image without ever running RasMol! See the Molecule to Image Converter Engine. 97/04/01: The broken downloading link for Win32SOle has been fixed. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: New Index to Chime/RasMol Tutorials Date: Mon, 7 Apr 1997 14:47:12 -0400 (EDT) To: rasmol@noc1.oit.umass.edu I've put my first draft of a World Index (I hope) to BioMolecular Structure Tutorials in Chime and RasMol at www.umass.edu/microbio/rasmol/tutbymol.htm Please tell me about resources I've overlooked. Note that I've limited my index to tutorials on BIOLOGICAL molecules -- unfortunately there are far too many good CHEMISTRY sites for me to index! For the sites I've managed to index, there are a total of 37 tutorials, mostly on different molecules. These comprise 9 RasMol scripts and the remainder Chime scripts. Chime's excellence for educational presentations is clearly making it worth the effort for more people to learn HTML and sometimes some javascript in addition to RasMol chemical script command language (the superset implemented in Chime). I've also reorganized the page formerly entitled 'RasMol in the Classroom', now 'BioMolecules in the Classroom ...." at www.umass.edu/microbio/rasmol/rasclass.htm (As always I've tried hard not to break any existing links to my site.) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol Other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/  ++++------+------+------+------+------+------+------+------+------+------+ From: dwrt@BPHVAX.biophysics.rochester.edu (Steve Dewhurst) Subject: Re: New Index to Chime/RasMol Tutorials Date: Mon, 07 Apr 1997 15:40:14 -0400 (EDT) To: rasmol@noc1.oit.umass.edu >I've put my first draft of a World Index (I hope) to BioMolecular Structure >Tutorials in Chime and RasMol at > >www.umass.edu/microbio/rasmol/tutbymol.htm > >Please tell me about resources I've overlooked. >Note that I've limited my index to tutorials on BIOLOGICAL molecules -- >unfortunately there are far too many good CHEMISTRY sites for me to index! Dear Eric I have a couple of CHIME presentations online, which appear to now be glitch-free. They include CD4 and RANTES as well as HIV protease (already on your list): http://www.urmc.rochester.edu/smd/mbi/grad/cd4frame.html http://www.urmc.rochester.edu/smd/mbi/grad/ranframe.html Best regards Steve Dewhurst ************************************************************************* Steve Dewhurst Associate Professor, Department of Microbiology & Immunology University of Rochester Medical Center 575 Elmwood Avenue, Room 5-8106, Box 672. Rochester, NY 14642 Tel.:(716)275-3216; FAX:(716)473-2361 OR 473-9573 http://www.urmc.rochester.edu/smd/mbi/steved.html ************************************************************************* ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: New Index to Chime/RasMol Tutorials Date: Tue, 8 Apr 1997 07:53:16 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Thanks very much for pointing them out. I ran the CD4 one and it looked great! They are now in the 'World Index'. I'll also add your class page to my 'immunology classes on the web' site www.umass.edu/microbio/immclass At 03:47 PM 4/7/97 -0500, you wrote: >>I've put my first draft of a World Index (I hope) to BioMolecular Structure >>Tutorials in Chime and RasMol at >> >>www.umass.edu/microbio/rasmol/tutbymol.htm >> >>Please tell me about resources I've overlooked. >>Note that I've limited my index to tutorials on BIOLOGICAL molecules -- >>unfortunately there are far too many good CHEMISTRY sites for me to index! > > >Dear Eric > >I have a couple of CHIME presentations online, which appear to now be >glitch-free. They include CD4 and RANTES as well as HIV protease (already >on your list): > >http://www.urmc.rochester.edu/smd/mbi/grad/cd4frame.html >http://www.urmc.rochester.edu/smd/mbi/grad/ranframe.html > >Best regards > >Steve Dewhurst > >************************************************************************* >Steve Dewhurst >Associate Professor, Department of Microbiology & Immunology >University of Rochester Medical Center >575 Elmwood Avenue, Room 5-8106, Box 672. Rochester, NY 14642 >Tel.:(716)275-3216; FAX:(716)473-2361 OR 473-9573 >http://www.urmc.rochester.edu/smd/mbi/steved.html >************************************************************************* > > ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Chime and Internet Explorer Date: Thu, 10 Apr 1997 14:04:27 -0500 (EST) To: [The following information comes from Bryan Van Vliet of MDLI and is forwarded to the RasMol list with his permission. -Eric Martz] Chime works with Internet Explorer today as a 2D and 3D renderer. However, the scripting capabilities of Chime are still not available from IE 3.0. We need 3 features in Internet Explorer: * Support for the EMBED tag option TYPE= in order that our plug-in can be instantiated without having to place a separate structure file on the host. For example, we use to instantiate a button which runs a RasMol Script and changes the display of Chime in another window. * Support for javascript: URL references. In Netscape you can reference a JavaScript method or command via the URL "javascript:{command}" from both a plug-in or even the Open command. We make use of this capability from our plug-in to make it possible to create some of the tutorials you see with Chime. * Full support for JavaScript (Microsoft's JScript is JavaScript 1.0 compatible and Navigator 3.0 supports JavaScript 1.1). We have been talking to Microsoft about the need for these features. We expect IE 4.0 to completely support JavaScript. We have been told by a Microsoft engineer that the first 2 problems have been addressed in IE 4.0, but we haven't had a chance to verify this. If we do get support for the above 3 items all of the tutorials using Chime should be able to run from either Navigator 3.0 and above or Internet Explorer 4.0. If plug-in support is not fixed in Internet Explorer 4.0 our backup plan is to provide "Chime Pro for ActiveX". We already have a version of Chime Pro as an ActiveX component which we will ship to customers in the next few months. We would rather not release an Internet version (it is targeted at corporate Intranets) of this plug-in for the simple reason that every tutorial creator would have to modify their tutorials so that one version supported ActiveX and one supported plug-ins. Here is an example of embedding a plug-in: Here is an example of embedding an ActiveX component: In lieu of full plug-in support in Internet Explorer, Eric Martz would have to provide some mechanism for writing the proper plug-in or ActiveX object tag in his tutorials depending on which browser was being used. Furthermore, if there was a problem with using ActiveX in JavaScript in IE 4.0, or some JavaScript feature he was depending on didn't work, he might have to rewrite his tutorials in VBScript and serve completely distinct pages depending on which browser was being used. And since the Macintosh is usually behind on features in Internet Explorer (one of the reasons IE 3.0 is so small compared to Navigator on the Mac is because Microsoft left out their JScript support and ActiveX isn't included by default) Eric might be left with some difficult choices on the Macintosh as far as IE is concerned. And, although Microsoft has hinted at UNIX support for IE, I have not seen a version nor am I confident that it would include ActiveX even if it was available, so he could never just write ActiveX/VBScript pages or ActiveX/JavaScript pages to serve to the Internet community. MDL would really like to be able to support IE fully today. Should we put out an ActiveX version of our plug-in and make people like Eric have to create 2 sets of tutorials, one for Internet Explorer and one for Navigator? IE is a nice web browser which almost supports plug-ins completely. If only Microsoft would finish its plug-in support the Internet community would be better served. I'd like to hear opinions on this subject. MDL wants to support the scientific community with our rendering technology, but in a rational way. Thanks, Bryan ------------------------------------------------------------------------ | Bryan Van Vliet bryan@mdli.com | | Project Manager, 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 | ------------------------------------------------------------------------ /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ References: <50668.emartz@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Chime and Internet Explorer Date: Fri, 11 Apr 1997 08:16:50 -0400 (EDT) To: rasmol@noc1.oit.umass.edu, emartz@microbio.umass.edu Excerpts from mail: 10-Apr-97 Chime and Internet Explorer by "Eric Martz"@microbio.um >[The following information comes from Bryan Van Vliet of MDLI and is >forwarded to the RasMol list with his permission. -Eric Martz] > > > MDL would really like to be able to support IE fully today. Should we > put out an ActiveX version of our plug-in and make people like Eric > have to create 2 sets of tutorials, one for Internet Explorer and one > for Navigator? I won't speak for Eric or whether he would "have to create 2 sets of tutorials", but no way will I ever be induced to go that route. Aside from the colossal hassle of actually implementing such nonsense, it would be retrograde progression in terms of what the WWW is all about. The problem is clearly with IE 3.0. When the geniuses in Redmond get around to implementing EMBED tag options and JavaScript comparable to Netscape 3.01, I would be happy to make small changes so that both browsers could be used on the same page. -Will McClure References: <50668.emartz@microbio.umass.edu> <50668.emartz@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Re: Chime and Internet Explorer Date: Fri, 11 Apr 1997 12:42:36 +0000 To: rasmol@noc1.oit.umass.edu I absolutely agree with the sentiments below. Internet "standards" are shaky enough as it is, we don't want them to break down even more so that all our stuff has to be produced in Navigator and MIE versions. >Excerpts from mail: 10-Apr-97 Chime and Internet Explorer by "Eric >Martz"@microbio.um >>[The following information comes from Bryan Van Vliet of MDLI and is >>forwarded to the RasMol list with his permission. -Eric Martz] >> >> >> MDL would really like to be able to support IE fully today. Should we >> put out an ActiveX version of our plug-in and make people like Eric >> have to create 2 sets of tutorials, one for Internet Explorer and one >> for Navigator? > > I won't speak for Eric or whether he would "have to create 2 sets of >tutorials", but no way will I ever be induced to go that route. Aside >from the colossal hassle of actually implementing such nonsense, it >would be retrograde progression in terms of what the WWW is all about. >The problem is clearly with IE 3.0. When the geniuses in Redmond get >around to implementing EMBED tag options and JavaScript comparable to >Netscape 3.01, I would be happy to make small changes so that both >browsers could be used on the same page. > >-Will McClure _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html References: <199703161659.LAA07690@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: tpthoms Subject: Rasmol 2.5 for XfreeOS/2 Date: Tue, 22 Apr 1997 00:25:44 -0400 To: rasmol@noc1.oit.umass.edu Hi! I finally finished the port of Rasmol 2.5 to Xfree86 for OS/2. It can be found at hobbes.nmsu.edu /incoming. Thanks to everyone that contributed. Travis Thoms ++++------+------+------+------+------+------+------+------+------+------+ From: "Orjan Hansson" Subject: Biomolecular Structures, a Chime Course Date: Tue, 22 Apr 1997 18:33:17 GMT+0100 To: rasmol@noc1.oit.umass.edu Dear Chime Users, I have developed a course on "Biomolecular Structures" which is described in more detail below. Any comments are highly appreciated! With best regards, Orjan Hansson Announcement ------------ "Biomolecular Structures" is an Internet course intended to be used as a computer-based laboratory exercise for undergraduate students in basic biochemistry. It was designed to accompany the textbook "Biochemistry (2nd ed.)", by C.K. Mathews and K.E. van Holde (Benjamin/Cummings, 1996), but can be used together with any introductory course on biochemistry and biophysics. The following topics are covered: 1. Amino acids 1.1 Movement, atom coloring and molecular representation 1.2 Chemical groups 1.3 Stereoisomers 1.4 Atom labelling 1.5 Side chain properties 2. Peptides 2.1 Primary sequence 2.2 Molecular dynamics 3. Proteins 3.1 BPTI 3.2 Hemoglobin 3.3 Plastocyanin 3.4 Alcohol dehydrogenase 4. Nucleotides 4.1 Chemical groups 4.2 AMP and dAMP 4.3 Purines 4.4 Pyrimidines in DNA 4.5 Pyrimidines in RNA 4.6 Nucleotide coenzymes 5. Nucleic acids 5.1 B-DNA 5.2 A-DNA 5.3 Z-DNA 5.4 Transfer RNA 5.5 A protein/DNA complex The course makes use of the Chemscape Chime plug-in and JavaScript 1.1. Thus, Netscape Navigator 3.0 is required. Particular attention has been paid to the design of the user interface so that students which are not so experienced with computers can navigate easily through the course. A form with simple questions is included and when the student has completed it, he/she can send it via Email to a teacher for marking. Extensive help is available to guide the user. During December 1996, some 200 biochemistry students ran the course as a 2.5 hour laboratory exercise in our computer lab. Their response was very positive. A link to the course can be found at the following URL: http://www.lundberg.gu.se/bcbp/edu/ Orjan Hansson E-mail: Orjan.Hansson@bcbp.gu.se Orjan Hansson, Ph.D. | E-mail: Orjan.Hansson@bcbp.gu.se Dept. of Biochemistry & Biophysics | or: bcbpoh@lundberg.gu.se Lundberg Institute | Tel: +46 31 773 39 29 Goteborg University and | Fax: +46 31 773 39 10 Chalmers University of Technology | WWW: http://www.lundberg.gu.se Medicinaregatan 9C, S-413 90 Goteborg (Sweden) ++++------+------+------+------+------+------+------+------+------+------+ From: baucom@gorby.UCSC.EDU (Albion Baucom) Subject: User File Upload CGI Program And Chime Date: Wed, 23 Apr 1997 20:47:08 -0700 To: rasmol@noc1.oit.umass.edu I was wondering if a CGI program existed that could be used to direct files set from a client to chime, that is a CGI program that would allow a user to specify a local file to view in Chime on a server. I am asking because I am in the process of developing a web site for protein sequence alignment assessment and would like the user to be able to upload their own file to the server for assessment (specifically a protein homolog used for threading). Thanks in advance. Albion E. Baucom baucom@gorby.ucsc.edu UC Santa Cruz 241B Sinsheimer Labs Santa Cruz, CA 95064 (408) 920-1616 ++++------+------+------+------+------+------+------+------+------+------+ From: Klaus Frommer Subject: Books about Molecular Modeling and Visualization Date: Thu, 24 Apr 1997 14:58:37 +0200 (MESZ) To: rasmol@noc1.oit.umass.edu I am an undergraduate student of biochemistry and that is why I have the following question: Can anyone recommend one or more introducing books about Molecular Modeling and Visualization for beginners? The literature I have found was either only for specialists in this field or was rather a collection of essays than an overall tutorial. Thanks for your advice in advance Klaus Frommer _________________________________________________________________________ Eberhard-Karls-University of Tuebingen, GERMANY _________________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: Lora Burgess Subject: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 09:33:05 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Hello, I am updating a review chapter for Bioinorganic Catalysis. We would like to incorporate nice black and white ribbon and string type pictures of metalloproteins into the chapter. I know that we can write a Molscript file from RasMol, and port it over to an SGI, but we produce everything on Macs in our lab. Is there a similar program for a Mac that we can use to get good postscript results for black and white printing? I am starting a new job next week, and will have limited time to get back up here to use an SGI. Id like to be able to work from home on my Mac. Lora *************************** Lora Burgess Dept. of Chemistry Johns Hopkins University 34th & Charles Sts. Baltimore, MD 21218 410-516-7937 *************************** ++++------+------+------+------+------+------+------+------+------+------+ From: pujadas@argo.urv.es (Gerard Pujadas) Subject: Re: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 18:18:45 +0200 To: rasmol@noc1.oit.umass.edu Hi, RasMac is the Mac version of RasMol. I have installed it in a SGI and in a PowerMac and it runs with exactly the same commands and syntax. > Hello, > I am updating a review chapter for Bioinorganic Catalysis. We >would like to incorporate nice black and white ribbon and string type >pictures of metalloproteins into the chapter. I know that we can write a >Molscript file from RasMol, and port it over to an SGI, but we produce >everything on Macs in our lab. Is there a similar program for a Mac that >we can use to get good postscript results for black and white printing? >I am starting a new job next week, and will have limited time to get back >up here to use an SGI. Id like to be able to work from home on my Mac. > Lora > Hope this helps. Regards from our little Mediterranean country !!! Gerard. *************************************************************************** * Gerard Pujadas * * Biotecnologia Computacional * * Dept. Bioquimica i Biotecnologia e-mail: pujadas@quimica.urv.es * * Univ. Rovira i Virgili phone: 34 77 559565 * * Pla=E7a Imperial Tarraco 1 fax: 34 77 559597 = * * 43005 Tarragona (CATALONIA) * * State: Spain (European Union) * *************************************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: User File Upload CGI Program And Chime Date: Thu, 24 Apr 1997 10:54:08 -0700 To: rasmol@noc1.oit.umass.edu At 08:47 PM 4/23/97 -0700, Albion Baucom wrote: > >I was wondering if a CGI program existed that could be >used to direct files set from a client to chime, that is >a CGI program that would allow a user to specify a local >file to view in Chime on a server. > I am asking because I am in the process of >developing a web site for protein sequence alignment >assessment and would like the user to be able to upload >their own file to the server for assessment (specifically >a protein homolog used for threading). > >Thanks in advance. > You should be able to upload any file (pdb/etc.) to the server using the HTML 'file upload' form element. (This allows the user to pick a file to be uploaded when the user clicks submit..) >From there you need a CGI program to write the file out from the submission, and then trigger your special programs, and then presumably the CGI program would output a HTML page which points to the results of the processing. I suspect that if you search on "CGI and file and upload" you should be able to find some example CGI programs which accept a uploaded file. MDL's Chemscape system, which works with Chime Pro and Netscape LiveWire, allow for pasting structures directly into Chime Pro and then having the structure uploaded to the server automatically when the form is submitted. (Because of performance reasons we do not use CGI, so I have no direct experience with the CGI solution for what you are asking for...)). -tim >Albion E. Baucom >baucom@gorby.ucsc.edu > >UC Santa Cruz >241B Sinsheimer Labs >Santa Cruz, CA 95064 >(408) 920-1616 > > ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne R Fiori Subject: Re: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 11:42:06 -0700 To: rasmol@noc1.oit.umass.edu >Hi, RasMac is the Mac version of RasMol. I have installed it in a SGI and >in a PowerMac and it runs with exactly the same commands and syntax. > Yes RasMol runs on the Mac, but there isn't a version of MolScript for the Mac. If you have network access to your SGI running MolScript, you can still work from home. Generate the MolScript input files using RasMac, upload them to the SGI, generate the postscript (or eps) file, drag that file back to your Mac, and preview it with GhostScript. It's a little slower than sitting on the SGI, but fast enough. You can get GhostScript from any Macintosh archive. > >> Hello, >> I am updating a review chapter for Bioinorganic Catalysis. We >>would like to incorporate nice black and white ribbon and string type >>pictures of metalloproteins into the chapter. I know that we can write a >>Molscript file from RasMol, and port it over to an SGI, but we produce >>everything on Macs in our lab. Is there a similar program for a Mac that >>we can use to get good postscript results for black and white printing? >>I am starting a new job next week, and will have limited time to get back >>up here to use an SGI. Id like to be able to work from home on my Mac. >> ++++------+------+------+------+------+------+------+------+------+------+ From: Ramiro Tellez Sanz Subject: Re: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 20:42:28 +0200 (DFT) To: rasmol@noc1.oit.umass.edu On Thu, 24 Apr 1997, Lora Burgess wrote: > > Hello, > I am updating a review chapter for Bioinorganic Catalysis. We > would like to incorporate nice black and white ribbon and string type > pictures of metalloproteins into the chapter. I know that we can write a > Molscript file from RasMol, and port it over to an SGI, but we produce > everything on Macs in our lab. Is there a similar program for a Mac that > we can use to get good postscript results for black and white printing? > I am starting a new job next week, and will have limited time to get back > up here to use an SGI. Id like to be able to work from home on my Mac. > Lora > > *************************** > Lora Burgess > Dept. of Chemistry > Johns Hopkins University > 34th & Charles Sts. > Baltimore, MD 21218 > 410-516-7937 > *************************** > > > Hi! I use RasMac 2.6, the Rasmol version for the Mac OS. It prints OK also in Postcript, but has a minor bugs regarding the Spacefill structures when printing under Postcript. Just try it. BTW, its faster and nicer than on the PC, of course! Regards from SPAIN Ramiro Tellez Sanz Dpto. Physical Chemistry University of Almeria SPAIN ingen.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Books about Molecular Modeling and Visualization Date: Thu, 24 Apr 1997 17:44:58 -0400 To: rasmol@noc1.oit.umass.edu Have you seen Branden and Tooze's excellent intro? It is very readable and full of great pictures. A new edition is due out this fall. Introduction to Protein Structure by Carl Branden and John Tooze At 02:58 PM 4/24/97 +0200, you wrote: > >I am an undergraduate student of biochemistry and that is why I have the >following question: > >Can anyone recommend one or more introducing books about Molecular >Modeling and Visualization for beginners? > >The literature I have found was either only for specialists in this field >or was rather a collection of essays than an overall tutorial. > >Thanks for your advice in advance > >Klaus Frommer > >_________________________________________________________________________ > >Eberhard-Karls-University of Tuebingen, GERMANY >_________________________________________________________________________ > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu www.umass.edu/microbio/rasmol/emartz.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Lora Burgess Subject: Re: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 23:01:45 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Many thanks to the replies about my question about a molscript equivalent. I didnt make it clear that I am using RasMac now, but want to print black and white representations of proteins such as Molscript can generate, for example 3D arrows to represent beta-sheets, etc. Wayne Fiori's suggestion may be the most workable- thanks for the tip about Ghostscript- I wasnt aware of that program. Lora *************************** Lora Burgess Dept. of Chemistry Johns Hopkins University 34th & Charles Sts. Baltimore, MD 21218 410-516-7937 *************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Books about Molecular Modeling and Visualization Date: Fri, 25 Apr 1997 12:04:10 +0100 (BST) To: rasmol@noc1.oit.umass.edu > >Can anyone recommend one or more introducing books about Molecular > >Modeling and Visualization for beginners? I'd also strongly recommend Eric Martz's recommendation of Brandon & Tooze as an excellent introduction to Protein Structure. Here are some of my other recommendations. Please note that these are my personal opinions and not those of my employer and I hope pretty much impartial. Molecular Modelling & Visualization: "Molecular Modelling: Principles and Applications", Andrew Leach, Longman, 595 pages, 1996. "Computer Aided Molecular Design", Jean-Pierre Douchet and Jacques Weber, Academic Press, 487 pages, 1996. "Protein Architecture: A Practical Approach", A.M. Lesk, IRL Press, 287 pages, 1991. Protein Structure: "Introduction to Protein Structure", Carl Branden & John Tooze, Garland Press, 302 pages, 1991 "Principles of Protein Structure", G.E. Schulz and R.H. Schirmir, Springer Verlag, 314 pages, 1979. Computer Graphics: "Computer Graphics: Principles and Practice", Foley, van Dam, Feiner and Hughes, 2nd Edition, Addison Wesley, 1174 pages, 1990 Biochemistry: "Biochemistry", Lubert Stryer, 4th Edition, Freeman, 1089? pages, 1995?. My apologies to anyone that I've missed out. I'd be very interested in hearing other peoples recommendations. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 764918 ++++------+------+------+------+------+------+------+------+------+------+ From: baucom@gorby.UCSC.EDU (Albion Baucom) Subject: Re: Books about Molecular Modeling and Visualization Date: Fri, 25 Apr 1997 07:47:00 -0700 To: rasmol@noc1.oit.umass.edu This is an interesting book I have come across which is specific to Molecular visualization: Data Visualization in Molecular Science: Tools for Insight and Innovation Jack E. Bowie, Ed. ISBN 0-201-58157-4 It may be a bit technical for a beginner, but is specific to just this type of work. Hope this helps. Albion E. Baucom baucom@gorby.ucsc.edu UC Santa Cruz 241B Sinsheimer Labs Santa Cruz, CA 95064 (408) 920-1616 ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Books about Molecular Modeling and Visualization Date: Fri, 25 Apr 1997 16:13:06 +0200 (MESZ) To: rasmol@noc1.oit.umass.edu > > > > >Can anyone recommend one or more introducing books about Molecular > > >Modeling and Visualization for beginners? > > I'd also strongly recommend Eric Martz's recommendation of Brandon & > Tooze as an excellent introduction to Protein Structure. Here are some > of my other recommendations. Please note that these are my personal > opinions and not those of my employer and I hope pretty much impartial. > > ... > My apologies to anyone that I've missed out. I'd be very interested in > hearing other peoples recommendations. Hello All, I'm also very interested in souch books. My personal tip is Molecular Modeling Basic Principles and Applications by H.-D Holtje and G. Folkers VHC, ISBN 3-527-29384-1 It seems to be a comprehensive book which explains "all" recent methods in modeling, Thanks, Arne ++++------+------+------+------+------+------+------+------+------+------+ From: Aguinaldo Robinson de Souza Subject: Re: Books about Molecular Modeling and Visualization Date: Sat, 26 Apr 1997 09:36:34 -0200 (GRNLNDDT) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Hi All, I recommend the book: Proteins. A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. by C.L. Brooks III, M. Karplus, B. M. Pettitt John Wiley & Sons ISBN 0-471-62801-8 (cloth) ISBN 0-471-52977-X (paper) That's a nice book about computer simulation of proteins. Dr. Aguinaldo Robinson Departamento de Quimica Universidade Estadual Paulista Bauru, Sao Paulo, Brazil 17033-360 Phone:(014) 230-2111 (ext. 134) FAX: (014) 230-4470 e-mail: arobinso@azul.bauru.unesp.br arobinso@rhodes.cenapad.unicamp.br ++++------+------+------+------+------+------+------+------+------+------+ From: Randy Bumgardner Subject: path length limitation in Netscape Date: Tue, 29 Apr 1997 14:27:01 -0700 To: rasmol@noc1.oit.umass.edu Cc: chime-feedback@mdli.com Eric Martz requested that I post this to the list to answer any questions, or potential questions, concerning problems with opening image files on the Mac. Apparently, if the path length to the html doc is longer than 256 characters, Netscape will give an error that it could not find the file. However, if the path length to the html doc it not longer than 256 characters, but the absolute path to an embedded image or structure is, Netscape will display the page without the image or structure. The reason for this is the way that the Mac OS handles filenames. However, one workaround I can suggest is not to nest documents too deeply in the directory structure, unless its absolutely necessary. Additional information from Roger Sayle: The reason for this is that in theory filenames on Apple Macintoshes can never be longer than 255 characters. All of the Macintosh operating system API calls pass their filename parameters as Str255, using the pascal convention that the first byte holds the string length. (In RasMol): The ConvertFilename routine is a port of the InsideMacintosh routine that used to return a Str255. Indeed in a similar routine "SetFileInfo" I convert a filename into a Str255 in order to set the file's icon. If current versions of the Mac OS can have FSS structures whose absolute filepath is longer than 256 characters, not only would bounds checks be needed (and the "buffer" and "Filename" arrays extended) but many of the file manipulation routines would have to parse the filename and traverse the directory tree until the remaining filepath was less than 255 characters in order call the MacOS API. Randy Bumgardner **************************************************** Randy Bumgardner MDL Information Systems (510) 895-1313, ext. 1172 Voice:(510) 357-2222, x1172 randyb@mdli.com **************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Rasmol Date: Tue, 29 Apr 1997 18:41:21 -0400 To: mriehl@wp.bsu.edu Cc: rasmol@noc1.oit.umass.edu At 04:56 PM 4/29/97 -0500, you wrote: >Hello -- > >I am a professor of chemistry at Ball State University in Muncie, IN, >and I have been using Chime to enhance my course web pages for the last >year. > >My question is this: I use PowerPoint in my lectures and I would like >to incorporate Rasmol into the presentations. PowerPoint 7.0 (Windows >95) has interactive settings which allows me to start Rasmol (with a >blank screen) by clicking on an icon, or to open a .PDB file in Rasmol >in the same manner. However, I do not know how to open Rasmol with a >specific .MOL file, display, background, etc. from PowerPoint. Is there >a way to do this? If not, is this a limitation of Rasmol or PowerPoint? > >Thanks for your help and suggestions. > >Matthew Riehl, Professor >Department of Chemistry >Ball State University >Muncie, IN 47306 >(765) 285-8074 > > It would help to know whether you are using Windows or Mac. If Windows, then each RasMol icon will have a working directory/folder. If this folder contains a file named RASMOL.INI, when RasMol starts up, it will do whatever commands are in the INI file. So it can contain a script with a load command and other commands which set up an initial view, or it can call another script. I've copied this to the RasMol email list in case others have more to add. I don't know any way to do this on a Mac but I don't know much about Macs. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: Re: Rasmol Date: Wed, 30 Apr 1997 09:13:06 +0100 To: rasmol@noc1.oit.umass.edu >>My question is this: I use PowerPoint in my lectures and I would like >>to incorporate Rasmol into the presentations. PowerPoint 7.0 (Windows >>95) has interactive settings which allows me to start Rasmol (with a >>blank screen) by clicking on an icon, or to open a .PDB file in Rasmol >>in the same manner. However, I do not know how to open Rasmol with a >>specific .MOL file, display, background, etc. from PowerPoint. Is there >>a way to do this? If not, is this a limitation of Rasmol or PowerPoint? An alternative suggestion Use Netscape as a presentation manager as in my lacrep presentation on Eric's tutorial page. I use it for presentation during lectures. Its not as glitzy as Powerpoint (but that is just to impress people) but it is far more useful (it can incorporate any movie, sound or chime plug-in) and allows you to use two frames (one for graphics and one for text). h Henry Brzeski Dept of Bioscience and Biotechnology The Todd Centre University of Strathclyde 31 Taylor Street GLASGOW G4 0NR Tel 0141-548 3727 Fax 0141 553 4115 ++++------+------+------+------+------+------+------+------+------+------+ From: "Martin Glancy" Subject: Producing .xyz animations Date: Wed, 30 Apr 1997 10:09:10 0000 To: rasmol@noc1.oit.umass.edu I work at the Exploratory Hands-on Science Centre in Bristol, UK - we may be using Chime to provide an explanatory display on molecules. Do you know of a reference to making XYZ animations? I specifically want to show atoms and small molecules joining to form larger molecules (up to ethanol). I have been able to make some simple files by manually altering and adding coordinates in a .xyz text file. (These are for intranet use - I do not intend to 'infect' reliable sources with these simulations.) Ideally I would like a simple method of producing these, or suggestions of sources of files. Martin Glancy, The Exploratory Science Centre Bristol Old Station, Temple Meads, Bristol BS1 6QU. UK Tel 0117 907 9000 Fax 0117 907 8000 email martin@exploratory.org.uk ++++------+------+------+------+------+------+------+------+------+------+ From: skg Subject: Re: Producing .xyz animations Date: Wed, 30 Apr 1997 11:48:42 -0700 To: rasmol@noc1.oit.umass.edu At 10:09 AM 4/30/97, you wrote: >I work at the Exploratory Hands-on Science Centre in Bristol, UK - we >may be using Chime to provide an explanatory display on molecules. > >Do you know of a reference to making XYZ animations? I specifically >want to show atoms and small molecules joining to form larger >molecules (up to ethanol). > A good place to start would be with re_view, a program that facilitates animation of xyz files. The problem is if you want to animate a reaction, you have to learn a little quantum chem & a program like mopac that generates reaction coordinates....it's really easy doing thermal vibrations, but in reactions you have to guesstimate the transition states, etc. There's lots of higher end programs that do this (eg gaussian) but they are very expensive. Re-view is cheap (there might even be a shareware version), and it has some ancillary programs that help generate reaction files, as well as some example reaction files that you can animate easily to see what they look like. My personal interest with re_view has been it's ability to port xyz files to povray so you can not only do interesting still graphics but high quality animation using povray, dta and a .flc file player (AAPlayer). I've had alot of fun creating "molecular movies" - you can add sound files if you like. Of course the povray image files are large - I've got about 100 megs of animation at this point! I'd really like to be competent at this myself - if you run accross other programs that generate reaction state animations, or if you become well versed in generating transition states, let me know, please! I'm learning slowly, but mopac isn't the most user friendly program (It is free, however!). In the meantime, check out re_view at: http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/ Have fun! "It would now be technically possible to unify the world, abolish war and poverty altogether, if men desired their own happiness more than the misery of their enemies" Bertrand Russel ++++------+------+------+------+------+------+------+------+------+------+ From: cole@chemcrys.cam.ac.uk Subject: RasWin question Date: Mon, 5 May 1997 11:50:45 +0100 To: rasmol@noc1.oit.umass.edu Dear All, I currently run rasmol on a machine running unix. I use Rasmol in tandem with a controller tcl script that communicates directly with Rasmol via a unix file pipe. In the tcl/tk language, file pipes have been ported to PCs running windows, however the behaviour of Raswin seems to be different: when I try to open rasmol on a file pipe, raswin automatically starts a controller window: is there a way of forcing raswin not to spawn this control window but accept its commnds directly from the file pipe? Jason ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Feedback from Chime Resources Date: Mon, 05 May 1997 10:29:44 -0400 To: dmix@kodak.com Cc: rasmol@noc1.oit.umass.edu, molinaro@cchem.berkeley.edu At 07:51 AM 5/5/97 -0400, you wrote: >First, thanks for providing your source code and examples. They >have been very helpful in understanding how to use Chime and the >scripting tools. > >Question for you... >Is it possible to have Chime separate a molecule (pdb file) into >separate pieces and have those pieces "come together" via a set >of move commands. I have found the define, select, and restrict >commands for operating on separate parts of the file, but I have >not been able to dissect a molecule and operate on separate pieces >simulaneously within the same Chime window. > >I would like to simulate synthesis of DNA from a template and >fragments. I considered using xyz files and an animation but >have not found a reasonable way to generate the xyz files. > >Thanks, >Dave Mix >dmix@kodak.com You are trying to move two sets of atomic coordinates independently (e.g. to dock two molecules). Unfortunately, neither RasMol nor Chime supports this, though I believe both plan to do so in the future. Marco Molinaro created a version of RasMol which does exactly this. It is very nice as far as it goes but has an unfortunate bug which limits its ability to support scripts under Windows ('zap' in a script causes a crash). You can find Molinaro's UCB RasMol at http://mc2.cchem.berkeley.edu/Rasmol/v2.6/ As for XYZ files, this has been discussed recently on the rasmol email list http://www.umass.edu/microbio/rasmol/raslist.htm to which I am copying this message. If you search the recent history, you will find links to methods for creating XYZ files. However, in order to do docking from an XYZ file in Chime, it seems to me that you would need software to save the atomic coordinates for the two molecules in a sequence of different distances. I don't believe you could do this with Molinaro's RasMol. Even for a single molecule, RasMol does not have an option to save the selected atoms as a PDB in a user-specified orientation (or even for the original origin). I hope this will be added in the future (please note Roger Sayle and Mike Hartshorn :-) ). WebLab (free, just released in version 2) does allow saving a selected atoms from a single molecule in a user-specified orientation. http://www.msi.com/ /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Dalke Date: Mon, 5 May 1997 11:01:36 -0500 To: rasmol@noc1.oit.umass.edu Re: Feedback from Chime Resources Eric Martz said: > You are trying to move two sets of atomic coordinates independently (e.g. > to dock two molecules). Unfortunately, neither RasMol nor Chime supports > this, though I believe both plan to do so in the future. As a way around the problem, I was wondering if there would be any way for the Java interface to Chime to be able to transfer a new coordinate set. Thus, Java would do the work of computing the paths for the different coordinate sets, and Chime would display the results. Andrew dalke@ks.uiuc.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasWin question Date: Tue, 6 May 1997 12:27:00 +0100 (BST) To: cole@chemcrys.cam.ac.uk Cc: rasmol@noc1.oit.umass.edu Hi Jason, > I currently run rasmol on a machine running unix. I use Rasmol in tandem > with a controller tcl script that communicates directly with Rasmol via a > unix file pipe. In the tcl/tk language, file pipes have been ported to PCs > running windows, however the behaviour of Raswin seems to be different: when > I try to open rasmol on a file pipe, raswin automatically starts a controller > window: is there a way of forcing raswin not to spawn this control window > but accept its commands directly from the file pipe? Unfortunately the problem is one of operating system philosophy rather than programming. Unlike UNIX, programs running on the Macintosh or under Microsoft Windows do not have a "default" controlling window, i.e. there is no equivalent of an "xterm" to type commands in from. Such programs have neither an input or output pipe (indeed C programs for Microsoft Windows can't call "printf"). Unfortunately the situation is confused by "MSDOS" which does have input and output pipes. However MSDOS programs aren't allowed to create their own windows etc... There is a possible solution. It is possible to communicate directly to RasWin using Microsoft DDE to both send commands and receive information about which atoms have been clicked. Hence most programs that attempt the things you are doing use Visual Basic, Word, Excel or similar package to send commands to RasWin. In addition there are a number of potential solutions on the horizon. On UNIX, RasMol supports Tcl/Tk's "send" mechanism for sending commands between Tcl/Tk program. In theory, RasWin should support Windows Tcl/Tk's "send" mechanism. Unfortunately Windows Tcl/Tk doesn't currently implement the send command. One solution is for me to contribute the necessary patches to SUN Microsystem to implement Tcl/Tk "send" using Microsoft DDE and make any changes necessary to RasWin to support it. Another possible course of action is to finish the support for WINSOCK sockets in RasWin to behave identically to the socket support in RasMol. This mechanism also allows commands to be passed to RasMol and information on clicked atoms to be passed back. A long term goal is to allow programs to communicate with RasMol on Mac, PC and UNIX from any program (on any host) using the same mechanism. One problem with this is that Windows Tcl/Tk doesn't yet support Sockets either... [One convience of such an approach is that it allows a Java/JavaScript Object/API to be defined that allows communication to either/both Chime and RasMol on all platforms]. To conclude, Windows Tcl/Tk does a very poor job of covering up the differences between UNIX and Windows with most useful functionality not implemented. Unless this changes its best to use a Windows supported languages on PCs and UNIX supported languages under UNIX. Please let me know which of the above suggestions merits the most attention. If its urgent, I expect we could provide "send" patches for tcl/tk within a month or two. And if anyone knows what SUN's plans to "send" and/or socket support in Windows Tcl/Tk are, or knows of unofficial send/socket patches, I'd be extremely interested in hearing from them. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 764918 X-Sun-Charset: US-ASCII ++++------+------+------+------+------+------+------+------+------+------+ From: cole@chemcrys.cam.ac.uk Subject: Re: RasWin question Date: Tue, 6 May 1997 17:09:46 +0100 To: rasmol@noc1.oit.umass.edu Dear All, Rogers more than encompassing reply to my earlier question has made me spend far to much time today trawlling the web looking for info about windows and Tcl/Tk. I've included any results of this below. If you are more the 'user' type of person of Rasmol, then I'd stop reading now. J. > Hi Jason, > > I currently run rasmol on a machine running unix. I use Rasmol in tandem > > with a controller tcl script that communicates directly with Rasmol via a > > unix file pipe. In the tcl/tk language, file pipes have been ported to PCs > > running windows, however the behaviour of Raswin seems to be different: when > > I try to open rasmol on a file pipe, raswin automatically starts a controller > > window: is there a way of forcing raswin not to spawn this control window > > but accept its commands directly from the file pipe? > > Unfortunately the problem is one of operating system philosophy rather > than programming. Unlike UNIX, programs running on the Macintosh or > under Microsoft Windows do not have a "default" controlling window, > i.e. there is no equivalent of an "xterm" to type commands in from. > > Such programs have neither an input or output pipe (indeed C programs > for Microsoft Windows can't call "printf"). Unfortunately the situation > is confused by "MSDOS" which does have input and output pipes. However > MSDOS programs aren't allowed to create their own windows etc... > I suspected as much. *I just wanted to be sure* > There is a possible solution. It is possible to communicate directly to > RasWin using Microsoft DDE to both send commands and receive information > about which atoms have been clicked. Hence most programs that attempt the > things you are doing use Visual Basic, Word, Excel or similar package to > send commands to RasWin. > > In addition there are a number of potential solutions on the horizon. > On UNIX, RasMol supports Tcl/Tk's "send" mechanism for sending commands > between Tcl/Tk program. In theory, RasWin should support Windows Tcl/Tk's > "send" mechanism. Unfortunately Windows Tcl/Tk doesn't currently > implement the send command. One solution is for me to contribute the > necessary patches to SUN Microsystem to implement Tcl/Tk "send" using > Microsoft DDE and make any changes necessary to RasWin to support it. > As you say, "send" is not directly supported in Windows Tcl/Tk. Current plans on Sun's Tcl/Tk home page seem to have swept it under the carpet, since the send command is very tied up with an X-server. Some ports are allegedly available for it though, although I've never tried them: e.g. here is a link to one: http://www.sunlabs.com/~kcorey/tcldde.html maybe I'll try it out. > Another possible course of action is to finish the support for WINSOCK > sockets in RasWin to behave identically to the socket support in RasMol. > This mechanism also allows commands to be passed to RasMol and information > on clicked atoms to be passed back. A long term goal is to allow programs > to communicate with RasMol on Mac, PC and UNIX from any program (on any > host) using the same mechanism. One problem with this is that Windows > Tcl/Tk doesn't yet support Sockets either... Sockets came into UNIX Tcl/Tk with version Tcl7.5/Tk4.1: I *think* that they have been ported to windows in later releases: I tried Tcl7.6/Tk4.2 and the commands are there (as opposed to send for example), but I've never used them in anger so this doesnt count as a full blown test. Is there somewhere where one can look to get info on UNIX rasmol's socket implementation? > > [One convience of such an approach is that it allows a Java/JavaScript > Object/API to be defined that allows communication to either/both Chime > and RasMol on all platforms]. > > > To conclude, Windows Tcl/Tk does a very poor job of covering up the > differences between UNIX and Windows with most useful functionality > not implemented. Unless this changes its best to use a Windows supported > languages on PCs and UNIX supported languages under UNIX. > Yes, but *wouldn't it be nice* to have just the one set of code: halves the job of maintenance and future development... > > Please let me know which of the above suggestions merits the most > attention. If its urgent, I expect we could provide "send" patches > for tcl/tk within a month or two. And if anyone knows what SUN's > plans to "send" and/or socket support in Windows Tcl/Tk are, or knows of > unofficial send/socket patches, I'd be extremely interested in hearing > from them. > I'm not sure which way we will go to be honest, so I cant say for me which suggestion merits most attention for me. I know that SUN are distributing PC ports of Tcl/Tk, but the home pages on the web dont give a lot away with regards to the directions they are planning to go in. I had more success looking at the WINTCL mailing list. http://www.smli.com/tcl/lists/WINTCL/index.html Best Wishes Jason ++++------+------+------+------+------+------+------+------+------+------+ From: baucom@gorby.UCSC.EDU (Albion Baucom) Subject: Hidden Chime Script Buttons Date: Wed, 7 May 1997 21:33:39 -0700 To: rasmol@noc1.oit.umass.edu I am having a lot of problems getting a hidden button (in a hidden frame) to execute. I have had no problem getting an tag to execute in a browser window with a push button, but when I create a hidden frame (no space allocated to it in the frameset) and use the immediate="true" the button will not execute. Is their a standard way to set up these "hidden" buttons that will make them execute (particulary when you are using JavaScript to write a new button to a hidden frame for immediate execution)? Thanks in advance ... Albion E. Baucom baucom@gorby.ucsc.edu UC Santa Cruz 241B Sinsheimer Labs Santa Cruz, CA 95064 (408) 920-1616 ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Hidden Chime Script Buttons Date: Thu, 08 May 1997 01:23:20 -0700 To: rasmol@noc1.oit.umass.edu Cc: chime-feedback@mdli.com At 09:33 PM 5/7/97 -0700, Albion Baucom wrote: > >I am having a lot of problems getting a hidden button (in a hidden frame) >to execute. I have had no problem getting an tag to execute in >a browser window with a push button, but when I create a hidden frame >(no space allocated to it in the frameset) and use the immediate="true" >the button will not execute. Is their a standard way to set up these >"hidden" buttons that will make them execute (particulary when you are >using JavaScript to write a new button to a hidden frame for immediate >execution)? > The only problem I am aware of in this area is in the SGI version of Netscape. If you make the chime plugin 'hidden' (using the hidden argument within the embed tag) the SGI version of Navigator never invokes the plugin, and so the button does not work. Eric has a nice JavaScript routine for sending a script to Chime, which takes care of writing the Chime button embed tag to a hidden frame, and this can be made to work on all Chime platforms by modifying it to *not* put the hidden attribute within the embed tag. (The button will still be hidden because it is within a hidden frame). Please let me know if this is *not* the problem you are seeing. -thanks, tim >Thanks in advance ... > > >Albion E. Baucom >baucom@gorby.ucsc.edu > >UC Santa Cruz >241B Sinsheimer Labs >Santa Cruz, CA 95064 >(408) 920-1616 > > ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Java interface for Chime Date: Thu, 08 May 1997 01:23:32 -0700 To: rasmol@noc1.oit.umass.edu At 11:01 AM 5/5/97 -0500, you wrote: >Re: Feedback from Chime Resources > >Eric Martz said: >> You are trying to move two sets of atomic coordinates independently (e.g. >> to dock two molecules). Unfortunately, neither RasMol nor Chime supports >> this, though I believe both plan to do so in the future. > > As a way around the problem, I was wondering if there would be >any way for the Java interface to Chime to be able to transfer a >new coordinate set. Thus, Java would do the work of computing >the paths for the different coordinate sets, and Chime would display >the results. The upcoming version of Chime does have the ability for atom coordinates to be updated. This is what the Sculpt Explorer uses to change the atom coords as the molecule is manipulated. We should be able to wrap this same mechanism up into the Chime Java interface which is also in development. Once a Java mechanism is available it should be possible to do many things, such as move multiple molecules within a chime window. Some very exciting new features are coming very soon in the upcoming beta of the new Chime. We will keep this list, as well as the Chime mailing list, posted on the developments. -tim > > Andrew > dalke@ks.uiuc.edu > > ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Clicking fails to report atom in Mac Chime (bug) Date: Thu, 08 May 1997 19:26:31 -0400 To: rasmol@noc1.oit.umass.edu In case anyone else is wondering, there is a bug in Macintosh Chime 1.0 which prevents it from reporting an atom you have clicked to the messages textarea if you have a command line interface (textarea target for MessageCallBack). This may have been announced here before, but if so I forgot and am announcing it again in case others also forgot. Tim Maffett says the bug is fixed in their development version but it will be awhile before MDL can release an updated Mac version for the rest of us. The default start-up mode of Chime is 'set picking ident'. The extent to which the 'picking ident' bug affects other 'set picking' options is not known to me. There appear to be no bugs for picking ident etc. in Windows 3.1 or Windows 95 versions of Chime. You can test this by going to the demo command line interface http://www.umass.edu/microbio/chime/chimehow/fs_cmdln.htm pressing the 'heme only' button, and clicking on any atom. (Smooth backbone traces can't report atoms.) A report should appear in the large box below the input box, and also on the Netscape status line (provided you leave the debugscript=on in the embed tag). More specifically, Tim says: " The mac version of Chime has the Y coordinate of the mouse inverted which it uses to identify the atom/residue when picking. If the atom is near the top of the window, and instead you click about the same distance away from the *bottom* of the window, you will get a picking ident report." So, it isn't a bug in YOUR javascript after all! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: Clicking fails to report atom in Mac Chime (bug) Date: Thu, 8 May 97 17:59:58 PDT To: rasmol@noc1.oit.umass.edu Eric, I've found the clicking function works with the Mac if you hold down the Control, Option, or Command Key first, although the Mac is very stubborn to respond to the Set Picking commands. I've finally learned how to implement your javascript and find it works much better when embedded in the HTML rather than having it called as a separate *.js file. (See temporary URL: http://mentor.lscf.ucsb.edu/mcdb133-X/chapter04/hel-1.htm). I find that when downloading a web page from the server and calling a *.js file at the same time, there seems to be a critical timing factor or "instability, particularly with the Mac, that very often leads to javascript errors. These are avoided (in my case at least) when the javascript is embedded directly in the HTML. Duane At 07:26 PM 5/8/97 -0400, you wrote: >In case anyone else is wondering, there is a bug in Macintosh Chime 1.0 >which prevents it from reporting an atom you have clicked to the messages >textarea if you have a command line interface (textarea target for >MessageCallBack). This may have been announced here before, but if so I >forgot and am announcing it again in case others also forgot. Tim Maffett >says the bug is fixed in their development version but it will be awhile >before MDL can release an updated Mac version for the rest of us. > >The default start-up mode of Chime is 'set picking ident'. The extent to >which the 'picking ident' bug affects other 'set picking' options is not >known to me. There appear to be no bugs for picking ident etc. in Windows >3.1 or Windows 95 versions of Chime. > >You can test this by going to the demo command line interface > >http://www.umass.edu/microbio/chime/chimehow/fs_cmdln.htm > >pressing the 'heme only' button, and clicking on any atom. (Smooth >backbone traces can't report atoms.) A report should appear in the large >box below the input box, and also on the Netscape status line (provided you >leave the debugscript=on in the embed tag). > >More specifically, Tim says: > >" The mac version of Chime has the Y coordinate of the mouse inverted >which it uses to identify the atom/residue when picking. If the atom is near >the top of the window, and instead you click about the same distance away >from the *bottom* of the window, you will get a picking ident report." > >So, it isn't a bug in YOUR javascript after all! >-Eric >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Eric Martz, Professor (Immunology), Dept Microbiology >Morrill IVN 203, U Mass, Amherst MA US 01003-5720 >413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu >RasMol Home Page http://www.umass.edu/microbio/rasmol >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Duane W. Sears | | Professor of Immunology and Biochemistry | | Department of Molecular, Cell, and Developmental Biology | | University of California Santa Barbara | | Santa Barbara, CA 93106 | | Telephones: | | Office: 805-893-3499 (answering machine) | | Lab: 805-893-4272 | | FAX: 805-893-4724 | | E-mail addresses: | | Faculty: sears@lifesci.lscf.ucsb.edu | | Academic: bioimages@lifesci.lscf.ucsb.edu | | WWW homepages: | | http://mentor.lscf.ucsb.edu/mcdb108a/ | | http://mentor.lscf.ucsb.edu/mcdb133/ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ References: <9705090059.AA13494@lifesci.lscf.ucsb.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Clicking fails to report atom in Mac Chime (bug) Date: Fri, 9 May 1997 10:22:35 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Excerpts from mail: 8-May-97 Re: Clicking fails to repor.. by Duane Sears@lifesci.ucsb > I've found the clicking function works with the Mac if you hold down the > Control, Option, or Command Key first, although the Mac is very stubborn to > respond to the Set Picking commands. I've found the same picking problem described by Duane, but the key commands "work around" are not reliable enough to use on a course page, e.g. for an interactive quiz. It will be great when the next version of Chime includes a fix. Another problem is the AnimFrameCallback. We wanted to show a simulated annealing sequence in connection with the NMR structure portion of a course. Some tests using the Raul E. Cachau helix unfolding sequence did not display correctly on the Mac. It worked fine on a SGI IRIX computer, however. JavaScript is used to provide a frame counter; i.e. a time indicator eventually. I don't know whether Windows will work on this, but if someone wants to try, look at: http://info.bio.cmu.edu/Courses/BiochemMols/XYZAnimJS.html I hope a fix to this problem is also included in the next Chime version. -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol email list is down Date: Tue, 13 May 1997 17:37:08 -0400 To: [270-some subscribers] Due to a hardware failure, the RasMol email list is temporarily out of service. We hope to have it back in action within a week. It is best not to send messages to the list address until the server is repaired. I'll post an announcement to subscribers via the list when it is back in service. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol email list is down Date: Tue, 13 May 1997 17:37:08 -0400 To: rbrzezin@courrier.usherb.ca, cupton@uvic.ca, michnick@BCH.UMontreal.CA, Due to a hardware failure, the RasMol email list is temporarily out of service. We hope to have it back in action within a week. It is best not to send messages to the list address until the server is repaired. I'll post an announcement to subscribers via the list when it is back in service. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: List is up again Date: Tue, 10 Jun 1997 12:33:43 -0400 To: rasmol@lists.umass.edu Cc: john@nic.umass.edu The RasMol email list has been down since May 12, 1997, due to a hardware failure. (Hope you all noticed how much you missed it! :-) It is now operational again, so feel free to send messages to the list. The list of subscribers current at the time of the failure was lost. The most recent backup I had was from February 6, 1997, and contained 276 subscribers. These 276 subscribers have been restored. Unfortunately a couple of dozen people who subscribed between 2/6/97 and the failure on 5/12/97 are no longer subscribed. If you happen to know of someone in this category, please alert them to the need to resubscribe. If you were getting your messages as a weekly digest instead of one at a time, you'll need to send (in the body of the message) set rasmol mail digest again, to listproc@lists.umass.edu As always, full information on the list, how to use it, and the message history, is 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 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Electrostatic Potential Date: Tue, 10 Jun 1997 13:34:26 -0400 To: rasmol@lists.umass.edu >Date: Thu, 5 Jun 1997 18:21:32 +0100 (BST) >From: Sayle Dr R A >To: Steve French >cc: Eric Martz >Subject: Re: Rasmol Elpot > > >Hi Steve, >> >commands recently and I came accross the "colour dots potential command". >> >When I saw this I was overjoyed because I have been trying to map the >> >electrostatic potential of different molecules. However, when I tried >> >using this command on proteins downloaded from Brookhaven they came out all >> >red. I also tried it on some of the carotenoids I have built using >> >Chemoffice 4.0 since I have read that potentials of proteins are not able >> >to be calculated yet. The carotenoids came out as all green. > >Thanks very much for your e-mail. Unfortunately, the problem is that >RasMol cannot determine the atomic partial charges on a molecule but can >make use of them if they are provided. For example, if they are placed >in the b-factor column of a PDB file. For example, the aspirin molecule >provided in Alchemy format with RasMol has charges stored in it which can >be used to colour dot surfaces. > >Without a doubt the best way to get extremely accurate co-ordinates and >charges for small molecules is to use a program such as MOPAC. Luckily >MOPAC is included with ChemOffice 4.0 (a public domain version for MSDOS >and UNIX is also available on the Internet). RasMol's MOPAC file format >reader can automatically extract charges when these are present in a >MOPAC output file. > >I wonder if it is possible to get ChemOffice to output charges in the >B-factor column of a PDB file? > > >I hope this helps. Please let me know how you get on. > >Roger >-- >Roger Sayle INTERNET: ras32425@ggr.co.uk >Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk >Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) >Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 764918 > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: LAANDERSSON@vassar.edu (LAURA A. ANDERSSON) Subject: Re: catalase tetramer Date: Tue, 10 Jun 1997 14:13:20 -0400 (EDT) To: rasmol@lists.umass.edu Hi, I'm a Rasmac user and am studying catalases {tetrameric heme proteins with each of the 4 subunits having a tyrosinate-linked heme moiety}. When I open up a file like 7cat.pdb (or any of the available catalas4e x-ray files) i get only a single subunit displayed, rather than seeing the whole protein. How can I see the tetramer? thanks in advance LAA ***** Laura A. Andersson, Ph.D. Department of Chemistry Vassar College Box 589 Poughkeepsie, NY 12604-0589 (914) 437-5747 FAX: (914) 437-5732 E.mail: LAANDERSSON@vaxsar.vassar.edu ***** ++++------+------+------+------+------+------+------+------+------+------+ From: Aidan Dysart Subject: Re: catalase tetramer Date: Tue, 10 Jun 1997 14:26:43 -0400 (EDT) To: rasmol@lists.umass.edu > I'm a Rasmac user and am studying catalases {tetrameric heme proteins > with each of the 4 subunits having a tyrosinate-linked heme moiety}. > When I open up a file like 7cat.pdb (or any of the available catalas4e > x-ray files) i get only a single subunit displayed, rather than seeing the > whole protein. > How can I see the tetramer? > thanks in advance My guess is that the file only contains the monomer. I don't know of any way to display multiple copies of the same file (or multiple files for that matter) in the same window. So, I would suggest looking for a pdb file (or other format) that contains the entire tetramer. If one doesn't exist, you could be really sneaky and try to write a program to generate the tetramer from the monomer by processing the file, but that would be alot of work. Anyway, be sure to check the Brrokhaven Protein Data Bank: http://www.pdb.bnl.gov/ +------------------------------------------+ | Aidan Dysart | | The University of Michigan | | adysart@umich.edu | | http://www-personal.umich.edu/~adysart/ | +------------------------------------------+ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: catalase tetramer Date: Tue, 10 Jun 1997 20:28:43 +0100 (BST) To: "LAURA A. ANDERSSON" Cc: rasmol@lists.umass.edu Dear All, > I'm a Rasmac user and am studying catalases {tetrameric heme proteins > with each of the 4 subunits having a tyrosinate-linked heme moiety}. > When I open up a file like 7cat.pdb (or any of the available catalase > x-ray files) i get only a single subunit displayed, rather than seeing the > whole protein. One resource that RasMol and Chime users may find useful is Brookhaven's database of proteins in their biological units. These files can be found at ftp://ftp.pdb.bnl.gov/user_group/biological_units/ Unfortunately, I couldn't see 7cat.pdb included in the list of files and the program I would normally use to scan for "catalase" seems to be hanging mysteriously. However I hope the above URL proves useful. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 764918 "Re: catalase tetramer" (Jun 10, 8:28pm) References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: catalase tetramer Date: Tue, 10 Jun 1997 17:17:45 -0400 To: "LAURA A. ANDERSSON" , rasmol@lists.umass.edu Cc: bryant@glowworm.nlm.nih.gov, hogue@glowworm.nlm.nih.gov Hi Laura The PDB list of biological units is, as Roger indicates, incomplete, and no effort on Brookhaven's part has been exerted to make it a complete reference or to incorporate it into their database. Instead I would point you to the EBI Mirror of PDB. You will find what you are looking for there! The EBI version of the PDB-3DB browser http://croma.ebi.ac.uk/pdb/cgi-bin/pdbmain (but not the Brookhaven version) can be used with the query 7CAT and the link "Complete MacroMolecule(s) for PDB entry 7cat" will give you the tetramer PDB file, just as you expect! Please visit the Crystal MacroMolecule Files at: http://croma.ebi.ac.uk/pdb/macmol_doc.html For details & credits. This is the most complete source regarding the creation of complete biological units of structure. Many, many thanks to the EBI structure team for this important work, and we look forward to rolling this data into MMDB's database in the future so that Cn3D will always show biological units by default. Christopher Hogue, NCBI On Jun 10, 8:28pm, Sayle Dr R A wrote: > Subject: Re: catalase tetramer > > Dear All, > > I'm a Rasmac user and am studying catalases {tetrameric heme proteins > > with each of the 4 subunits having a tyrosinate-linked heme moiety}. > > When I open up a file like 7cat.pdb (or any of the available catalase > > x-ray files) i get only a single subunit displayed, rather than seeing the > > whole protein. > > One resource that RasMol and Chime users may find useful is Brookhaven's > database of proteins in their biological units. These files can be found > at ftp://ftp.pdb.bnl.gov/user_group/biological_units/ > > Unfortunately, I couldn't see 7cat.pdb included in the list of files and > the program I would normally use to scan for "catalase" seems to be > hanging mysteriously. However I hope the above URL proves useful. > > Roger > -- > Roger Sayle INTERNET: ras32425@ggr.co.uk > Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk > Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) > Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 764918 >-- End of excerpt from Sayle Dr R A -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Christopher Hogue, Ph.D. National Center for Biotechnology Information National Library of Medicine, National Institutes of Health Bldg 38A 8600 Rockville Pike, Bethesda MD 20894 hogue@ncbi.nlm.nih.gov voice (301) 496-2477 x282 fax (301) 435-2433 http://www.ncbi.nlm.nih.gov/Structure ~~~~MOVING ---> July 1 to Toronto See http://www.ncbi.nlm.nih.gov/Structure/alumni.html for details as they become available. ++++------+------+------+------+------+------+------+------+------+------+ From: Warren Gallagher Subject: Re: catalase tetramer Date: Wed, 11 Jun 97 08:25:04 -0500 To: rasmol@lists.umass.edu 10. June, 1997 Laura, Re: > I'm a Rasmac user and am studying catalases {tetrameric heme proteins >with each of the 4 subunits having a tyrosinate-linked heme moiety}. > When I open up a file like 7cat.pdb (or any of the available catalas4e >x-ray files) i get only a single subunit displayed, rather than seeing the >whole protein. > How can I see the tetramer? >thanks in advance In the REMARK section of the 7cat.pdb file, Fita and Rossmann indicate they assumed that all four monomers were indentical during the refinement of the 7cat structure. They discuss how the coordintates for the other three momoners can be generated from the coordinates of the monomer given in 7cat.pdb. They indicate that they also did the refinement without assuming the monomers are identical. The results of this refinement, with all four of the tetramers present, is deposited in the Protein Data Bank as 8cat.pdb. "Re: catalase tetramer" (Jun 10, 2:13pm) References: <01IJWS82L1AA001DO8@VASSAR.EDU> ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: Re: catalase tetramer Date: Wed, 11 Jun 1997 16:01:15 -0400 To: rasmol@lists.umass.edu Dear Laura, The PDB has a directory of Prepared Biologically Functional Molecules that we have individually generated based on the biological information and symmetry. While not a complete collection yet, we are working on building this up. Any requests for specific molecules will be handled,as well. Please contact the PDB Help Desk, pdbhelp@bnl.govt. While the ftp URL given by Roger Sayle is correct, you will find this index on our Web site more useful: http://www.pdb.bnl.gov/biomol.html >From our Home Page, http://www.pdb.bnl.gov, click on Searching and Browsing the PDB, then on Indexed list of prepared Biological Molecules. The 3DB Browser points to this file if it exists for a selected entry. Also, as Christopher Hogue pointed out, the EBI has prepared a complete collection of macromolecules generated from the symmetry transformations, at http://croma.ebi.ac.uk/pdb/macmol_doc.html. Regards, Nancy On Jun 10, 2:13pm, LAURA A. ANDERSSON wrote: > Subject: Re: catalase tetramer > Hi, > I'm a Rasmac user and am studying catalases {tetrameric heme proteins > with each of the 4 subunits having a tyrosinate-linked heme moiety}. > When I open up a file like 7cat.pdb (or any of the available catalas4e > x-ray files) i get only a single subunit displayed, rather than seeing the > whole protein. > How can I see the tetramer? > thanks in advance > LAA > ***** > Laura A. Andersson, Ph.D. > Department of Chemistry > Vassar College > Box 589 > Poughkeepsie, NY 12604-0589 > (914) 437-5747 > FAX: (914) 437-5732 > E.mail: LAANDERSSON@vaxsar.vassar.edu > ***** >-- End of excerpt from LAURA A. ANDERSSON -- _______________________________________________________________________ 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: Andrey V Khavryutchenko Subject: write command disabled in scripts Date: Sun, 15 Jun 1997 18:45:39 +0200 (GMT+0200) To: rasmol@lists.umass.edu Hi! Does anyone knows what was the reason of disabling the 'write' and its equivalent 'save' commands in scripts? I'm talking about rasmol 2.6 b1 and b2, don't know about other versions. SY Andrey V Khavryutchenko akhavr@compchem.kiev.ua Std. Disclaimer: My opinions only. Don't take life too seriously, you don't get out of it alive anyway Burt Ward ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: write command disabled in scripts Date: Mon, 16 Jun 1997 15:50:17 +0100 (BST) To: Andrey V Khavryutchenko Cc: rasmol@lists.umass.edu Hi Andrey, > Does anyone knows what was the reason of disabling the > 'write' and its equivalent 'save' commands in scripts? The inability to use the save and write commands in a RasMol script file is a deliberate security feature. There was a concern about the security of using RasMol on the Internet when researchers started e-mailing and FTPing 'untrusted' script files between sites. This was especially true of sites that have configured Netscape to fire up RasMol with a RasMol script file MIME type. Such a script, executed with "rasmol -script " may potentially overwrite system and user files, for example creating a "~/.rhosts" or "/etc/passwd" file on the remote machine. To defend against this threat I decided to disable the save and write commands from within RasMol, unless the command "set write true" had been explicitly typed interactively on the command line. This restriction is very similar to that for Java applets which aren't allowed to create files on a local machine from within a Java applet. This may seem like a UNIX-only feature, but malicious scripts could overwrite system files or startup files on any system. It is still possible for people to create animations using RasMol, writing out an image file for each frame. The secret is that you must interactively type "set write true" to enable writing from scripts. Of course the "set write true" command is also disabled in scripts. Note that unlike RasMol's scripting language, a large number of scripting languages (such as AppleScript, sh, csh, perl, standard Tcl, Tripos SPL, Biosym BCL, Microsoft Word etc...) are potentially unsafe and should be used with extreme caution configured as helper applications under the WWW. Another UNIX security feature is that RasMol is unable to decompress files whose filenames contain special characters. For example, a valid set of compressed co-ordinates may be stored in the file "rm *;.pdb.gz" but RasMol will refuse to read them due to the way it decompresses files. Interestingly, Chime is able to read from such files without violating security due to the way it decompresses files! Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 764918 ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: RasMol Manual Date: Mon, 16 Jun 1997 16:05:16 -0400 (EDT) To: rasmol@lists.umass.edu RasMol Users, I recently divided rasman.htm into 22 files for faster navigation in a frames or linked page format. Except for the additions listed below, very little was changed in the content or format of the original hypertext version of the Manual. The URL for viewing or downloading is: http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/RASMAIN.HTM -Will McClure >From the Introduction: The following pages were added to the frames version. 1. A two-page PDF version of the "RasMol Quick Reference Card". 2. A page illustrating the Pull Down Menu selections. 3. A Summary Table of amino acid classes. 4. Three tables that display Predefined Colors, Amino/Shapely Colors, and CPK Colors. 5. A page on Files and File Formats from the v2.5 Manual and v2.6 update. A PDP file Example page with a glossary of terms is also linked to this page. 6. The Bibliography from the v2.5 Manual with links to some of these references in the text. ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Explorer and Chime/Rasmol Date: Thu, 19 Jun 1997 12:01:30 +0100 To: rasmol@lists.umass.edu Does anyone know if the latest release of Explorer supports Chime scripts (3.0 doesn't)? Also, a user here has problems with Explorer and RasWin as a helper app. Files come across, RasWin (32bit version) opens but doesn't load the file and gives: "can't find C:\winNT\temporary file" and the image window is black. Any clues. _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Compiling Rasmol under Debian Linux 1.2.4 16 bpp Date: Fri, 20 Jun 1997 02:12:08 +0200 To: rasmol@lists.umass.edu Hi all, I tried to compile Rasmol (V2.5 I think) under Debian-Linux 1.2.4 running a 16 bpp X-Server. Everything went fine so far, except, that the program wonīt start with 16 bpp color-depth. I can remember, that someone stated, that the actual version of Rasmol can be run on 16 bpp screens. Is there any known workaround, or have I messed up something (or simply forgotten to set some switch or alter something manualy)? Thanks in advance! References: <33A9CAD8.DDF7D924@rz.ruhr-uni-bochum.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: Compiling Rasmol under Debian Linux 1.2.4 16 bpp Date: Sat, 21 Jun 1997 18:33:04 +0200 To: rasmol@lists.umass.edu Aww, I made a little mistake: The version is 2.62b2, thatīs what the gz-file is named! -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/ ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Compiling Rasmol under Debian Linux 1.2.4 16 bpp (fwd) Date: Sun, 22 Jun 1997 13:56:42 +0200 (MESZ) To: rasmol@lists.umass.edu (to all MailingList) Forwarded message: > From owner-rasmol@lists.umass.edu Fri Jun 20 20:32:53 1997 > Delivery-Date: Fri, 20 Jun 1997 20:32:53 +0200 > Message-Id: <33A9CAD8.DDF7D924@rz.ruhr-uni-bochum.de> > Date: Fri, 20 Jun 1997 02:12:08 +0200 > Reply-To: Marc.Saric@rz.ruhr-uni-bochum.de > Sender: owner-rasmol@lists.umass.edu > From: Marc Saric > To: rasmol@lists.umass.edu > Subject: Compiling Rasmol under Debian Linux 1.2.4 16 bpp > MIME-Version: 1.0 > Content-Type: text/plain; charset=iso-8859-1 > X-Mailer: Mozilla 4.0 [en] (Win95; I) > X-Priority: 3 (Normal) > X-Listprocessor-Version: 8.1 -- ListProcessor(tm) by CREN > Content-Transfer-Encoding: quoted-printable > X-MIME-Autoconverted: from 8bit to quoted-printable by dhcp-srv2.oit.umass.edu > id OAA15502 > > Hi all, > > I tried to compile Rasmol (V2.5 I think) under Debian-Linux 1.2.4 > running a 16 bpp X-Server. > Everything went fine so far, except, that the program won=B4t start with > 16 bpp color-depth. > I can remember, that someone stated, that the actual version of Rasmol > can be run on 16 bpp screens. > > Is there any known workaround, or have I messed up something (or simply > forgotten to set some switch or alter something manualy)? > > Thanks in advance! > > Hello all, I built a 16 bit RasMol Version under linux, but rasmol shows me the following message: bash$ ./rasmol RasMol Molecular Renderer Roger Sayle, August 1995 Version 2.6 [24bit version] ... never mind it is a 16 bit version (it runs only on a 16 bit X-Server). Edit rasmol.h: /* rasmol.h * RasMol2 Molecular Graphics * Roger Sayle, August 1995 * Version 2.6 */ /*===========================*/ /* User Definable Options! */ /*===========================*/ /* #define IBMPC */ /* #define APPLEMAC */ /* #define DIALBOX */ #define TERMIOS #define SOCKETS #define MITSHM #define SIXTEENBIT /* #define MMIOLIB */ /* #define OMLCOMMS */ /* #define CEXIOLIB */ /* Use Default Depth! */ /* #define THIRTYTWOBIT */ /* #define EIGHTBIT */ /* use a sexteen bit display! */ #define SIXTEENBIT ... and recompile yout RasMol Arne References: <9706221156.AA58808@gwdu08.gwdg.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: Compiling Rasmol under Debian Linux 1.2.4 16 bpp (fwd) Date: Mon, 23 Jun 1997 15:14:18 +0200 To: rasmol@lists.umass.edu Thanks for the answer! Arne Mueller wrote: > > Edit rasmol.h: > /* #define IBMPC */ (..) > #define SIXTEENBIT (..) > /* use a sexteen bit display! */ > #define SIXTEENBIT > > ... > > and recompile yout RasMol Have done that (i.e. like it is stated in the INSTALL-text:[1] xmkmf, [2] edit rasmol.h, [3] make), but it didnīt worked. Then I tried to edit the Imakefile (there is also an #define -DEIGHTBIT (or -DTHIRTYTWOBIT), so I replaced it with -DSIXTEENBIT, compiled it and-- it worked! There are still some problems though: During compilation, I got some error messages stating something about -DSIXTEENBIT (have forgotten the exact reading, if you or someone else need it, I will look it up). Inspite of this, the program starts when typing "rasmol" at the prompt. When I load an *.pdb (tried the famous 1crn.pdb for a start) and try to display it as ribbon with colours set to "temperature" it gives me some weird colormapping (this does not happen with every color option -"cpk" or "structure" works fine most of the time). I use Afterstep as default window-manager, this one is known to take up many colors for its high-color-icons and bitmaps -could this be the reason for the color problems of 16-bit-rasmol?? Another thing is, that the border of the graphics-window is brown -realy ugly :-) Even if this is not of great importance, it would be nice to have another color (grey for example :-). Where can I change this (or is this my fault (i.e. something in my libraries or so))?? -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/ ++++------+------+------+------+------+------+------+------+------+------+ From: Slaton Lipscomb Subject: displaying 2D models and slabbing on Mac Date: Mon, 23 Jun 1997 21:41:11 -0800 To: rasmol@lists.umass.edu I have a couple of questions for the Chime experts out there. First, I have not found in the Chime documentation how to display a molfile in 2D rendering. This is an option in the MDL menu that is only available for molfiles (not for pdb). However there is no option for this in the display3d or options3d attributes for the element. Does anyone know an attribute for to have a molfile Chime model initially displayed in 2D rendering? Second, I have been unable to get the slabbing mouse/keystroke combination to work in Chime for the Macintosh. I have tried this on several different machines. According to the Chime and Rasmol documentation I have seen, ctrl is the key to hold down to engage slabbing with the mouse button held down over a Chime model (on Windows I believe it is ctrl-left click). When I hold down ctrl, mouse-click, and try to rotate the model, the model is frozen and occasionally rotates in sporadic twitches. This is a completely different effect from the engagement of slab plane from the MDL menu (and completely useless). Does anyone know the correct keystroke for slabbing on the Mac? Or does anyone's experience contradict mine? Thanks for your experise. Slaton Lipscomb C4: Computers in Chemistry at Cabrillo College http://www.cabrillo.cc.ca.us/c4/ ++++------+------+------+------+------+------+------+------+------+------+ From: Randy Bumgardner Subject: Re: displaying 2D models and slabbing on Mac Date: Tue, 24 Jun 1997 15:26:11 -0700 To: rasmol@lists.umass.edu At 10:41 PM 6/23/97 -0700, you wrote: >I have a couple of questions for the Chime experts out there. > >First, I have not found in the Chime documentation how to display a >molfile in 2D rendering. This is an option in the MDL menu that is only >available for molfiles (not for pdb). However there is no option for >this in the display3d or options3d attributes for the element. >Does anyone know an attribute for to have a molfile Chime model >initially displayed in 2D rendering? > Correct, there is no 2D attribute for the embed tag. Chime will display a molfile in two dimensions if the coordinates for the structure are 2D, ie, if the z coordinate is zero. This occurs if the structure is created in a drawing program, ISIS/Draw for example, and exported as a molfile. > >Second, I have been unable to get the slabbing mouse/keystroke >combination to work in Chime for the Macintosh. I have tried this on >several different machines. According to the Chime and Rasmol >documentation I have seen, ctrl is the key to hold down to engage >slabbing with the mouse button held down over a Chime model (on Windows >I believe it is ctrl-left click). When I hold down ctrl, mouse-click, >and try to rotate the model, the model is frozen and occasionally >rotates in sporadic twitches. This is a completely different effect from >the engagement of slab plane from the MDL menu (and completely useless). >Does anyone know the correct keystroke for slabbing on the Mac? Or does >anyone's experience contradict mine? > To move the clipping plane through the structure while in slab mode, the keystroke/mouse combination is '/left mouse button' for Windows, and '/mouse button' for the Mac. Slab mode must be selected from the Chime menu, and both the mouse button and the () key must be held down during the movement. On the Mac, a slight rotation does occur while moving the clipping plane. > >Thanks for your experise. > >Slaton Lipscomb >C4: Computers in Chemistry at Cabrillo College >http://www.cabrillo.cc.ca.us/c4/ > Randy **************************************************** Randy Bumgardner MDL Information Systems (510) 895-1313, ext. 1172 Voice:(510) 357-2222, x1172 randyb@mdli.com **************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Harry Ungar Subject: New Chime Tutorial Date: Tue, 24 Jun 1997 21:17:04 -0400 (EDT) To: rasmol@lists.umass.edu I invite all members of this list who use Netscape Navigator to take a look at our just completed "Chime Tutorial" at www.cabrillo.cc.ca.us/C4. This self-guided tutorial, created for beginning students, specifically shows how to use Chime molecular models and gives students a few glimpses into the potential power and beauty of molecular modeling. We hope that you will recommend the tutorial to your students, that you will link your web pages to it, and/or that you will download it for use on your own computers. This tutorial is the first product of C4 (Computers in Chemistry at Cabrillo College) and is supported by a grant from the National Science Foundation. All future C4 software will also be distributed over the World Wide Web so that it will immediately be available to everyone interested in using it. All C4 software can be used and reproduced without cost, provided it is for non-commercial purposes only. Harry Ungar C4: Computers in Chemistry at Cabrillo College 6500 Soquel Dr. Aptos, CA 95003 408-479-5059 http://www.cabrillo.cc.ca.us/CWIS/AcademicPrograms/BECHO/Chemistry/organic/i ndex.html. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime problems in 'secure' student computer labs Date: Fri, 27 Jun 1997 17:26:01 -0400 To: rasmol@lists.umass.edu Cc: stolle@cs.umass.edu, bbotch@chem.umass.edu, sbrewer@bio.umass.edu Dear Chimeleons: I'd like to find out how many student computer labs can't run my javascript-laden Chime tutorials, notably http://www.umass.edu/microbio/chime/protsecs (Protein Secondary Structure) and http://www.umass.edu/microbio/chime/dna (the AT or GC base pair buttons are good ones to test here as they use lots of javascript) If you can run these two tutorials on your private computer but not on the computers in your student lab(s), I'd like to know. Also if you have time I'd like to know: in what way does the tutorial fail to work properly or what error message(s) occur? Are you using macs or windows? What kinds of security precautions/software might be responsible? (Ask your lab installation manager.) If you get the same 'cannot open' error message I get, you might try going into the debug mode and seeing what exactly Chime reports it 'cannot open'. I've recently learned that such problems occur in our Chemistry Department's student computer lab. In our case, as I understand it, the security precautions employed are not Netscape Options menu items (such as disabling javascript), but rather some kind of security program is running in the background and intercepting operations deemed dubious. The effect is that when one attempts to run these tutorials, a "Javascript Alert" message occurs frequently reporting a "cannot open" message from Chime. I haven't yet been able to diagnose whether this message is real or a spurious symptom of problems I didn't anticipate when I wrote the code. But it doesn't happen on computers outside the student lab (which don't have the same security measures). My tutorials utilize javascript "cookies" to remember the states of variables between different Netscape windows. Cookies are saved by writing a file to disk. Cookie writing may be what is being intercepted. (A common use of cookies is to remember the contents of a shopping cart at a commercial website.) In any case, I'd like to assess the magnitude of the problem and if large, then work on solutions. For example, if cookies are the problem, I may be able to use global variables instead. (I had trouble figuring out how to do that which is why I resorted to cookies. In particular I could not figure out how to assign a name to the initial/default Netscape window, hence could not reference its variables from other windows.) I'll summarize the replies I get and post the summary to this list. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime problems in 'secure' student computer labs Date: Fri, 27 Jun 1997 18:47:31 -0400 To: rasmol@lists.umass.edu Cc: stolle@cs.umass.edu, bbotch@chem.umass.edu, sbrewer@bio.umass.edu Dear Chimeleons: With regard to my recent request about to finding out how many student computer labs can't run my javascript-laden Chime tutorials, please >>> use Netscape 3.01 ONLY <<< if you run such tests. We already know that some plug-in bugs were fixed since Netscape 3.00, and that Netscape 4 does not yet work as well as 3.01 with Chime, and that Internet Explorer works poorly with Chime. See recent history of this list for more details on these issues. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <3.0.1.32.19970627172601.00685bac@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Chime problems in 'secure' student computer labs Date: Mon, 30 Jun 1997 12:51:53 -0400 (EDT) To: rasmol@lists.umass.edu Excerpts from mail: 27-Jun-97 Chime problems in 'secure' .. by Eric Martz@microbio.umas > I'd like to find out how many student computer labs can't run my > javascript-laden Chime tutorials, notably > > http://www.umass.edu/microbio/chime/protsecs > (Protein Secondary Structure) > > and > > http://www.umass.edu/microbio/chime/dna > (the AT or GC base pair buttons are good ones to test here as they use lots > of javascript) > The .../dna page works fine on our student Macs. The .../protsecs has the same button problems from a few months ago. Is there a problem with allowing "resizing" in this frameset? As I recall, you wanted to keep the preset proportions as a model for lecture display where the image should be the main feature. But if resizing were allowed in the Web version, it would add some desirable flexibility in the viewing. -Will ++++------+------+------+------+------+------+------+------+------+------+ From: "Craig T. Martin" Subject: Several questions Date: Mon, 30 Jun 1997 17:53:05 -0400 To: rasmol@lists.umass.edu I have three questions for the Rasmol group: 1) In CHIME, is it possible from a single HTML embed call (eg., when setting up a window, as in the code below) to load a .pdb file and then run a script from an external file? I can embed the script within the call, but I would prefer to have a separate script file called "Reset.spt" which both initially sets up the view and can be called by a reset button (yes, I know that one could simply reload the structure, but I'm looking for something more elegant). I could load the molecule from within the script, but I have not been able to set up a CHIME window with reference to only a script. 2) I always compress my PDB files with GZIP (on the Mac) and then upload them (binary xfer) to my Unix server. Works great. However, those same "zipped" files are not recognized by CHIME if I load them directly from my local (Mac) disk. Is this a "feature"? 3) In a HTML file which both initializes a JavaScript function (via a call to an external text file) and loads a structure into the same frame, I occasionally get the JavaScript text loading into the CHIME window instead of the structure. The HTML file looks like the following: ----------------- Load Structure