Re: [Jmol-users] partial charges
On Sep 19, 2008, at 10:12 PM, Robert Hanson wrote:
The way to get partial charge data into .pdb files is to put it in
the temperature field. You can do that with:
{*}.temperature = {*}.partialcharge.all
Which will work on the revised Jmol that I haven't uploaded yet.
Which suggests to me that you might also try this in the version you
have:
{*}.partialcharge = {*}.property_partialcharge.all
That copies all the property_partialcharge data into the real
partialcharge field of the atoms.
Then do the isosurface MEP business.
Yes, this works perfectly for displaying the mep surface- beautiful!
And being able to get the values into the pdb file will be terrific.
Thanks,
Frieda
On Sep 13, 2008, at 1:00 PM, Robert Hanson wrote:
If that's all you want to do, try this:
load .pdb
set propertydatafield 9
x = load(.mol2)
data property_partialcharge @x
color property_partialcharge
//
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//
-
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Re: [Jmol-users] identifying proteins in mol2 files
OK, I will look into this. Frieda On Sep 10, 2008, at 2:10 PM, Robert Hanson wrote: We could set up the mol2 reader to do this. BUT I have to be convinced first that it's a real standard. What programs write these? Is it just totally arbitrary what these IDs are? Are the names standard? Try some more unusual structures, like DNA, RNA, nonstandard amino acids, 1BLU with its FeS4 sites. Hemoglobin. On Wed, Sep 10, 2008 at 8:51 AM, Angel Herraez [EMAIL PROTECTED] wrote: Dear Frieda I've never tried that. From the doc http://www.tripos.com/data/support/mol2.pdf it seems that atoms can have IDs and residue IDs; they quote an example: 1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000 BACKBONE|DICT|DIRECT 1 CA -0.149 0.299 0.000 C.3 [...] the atom is named CA and is [...] It belongs to the substructure with ID 1 which is named ALA1. So, Jmol should be able to interpret that, but maybe the file reader has not been set for that. As far as I know, the protein is determined based on bonding and key atom names (N, CA, C) within the same residue. Similarly for residue names. A quick test with a pdb file read into Accelrys DS Viewer 1.7 and saved into mol2 shows that the atom IDs are read in Jmol (example: select *.CA works), but not recognized as protein. select ala doesn't work either. So maybe it's just the residue ID part that is not being interpreted. Notably, that goes after the coordinates, rather than before them as in pdb. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol app - size of start-up window
Hi, can someone remind me of how to tell the Jmol app to open its display window to a certain width and height? All I can find in the archives is the following post, which seems no longer to have an effect, and the scripting documentation is still unavailable (and I'm not too hopeful it would be in there)... Tim wrote: By the way is there a command-line option for adjusting the window size at start-up? No, but that is a very good idea. I just checked in code to allow one to set the window size on the Jmol application command-line: -g WIDTHxHEIGHT or --geometry WIDTHxHEIGHT Where WIDTHxHEIGHT is the width and the height in pixels separated by a lower case 'x' 500x550 (the current default) 300x350 (something smaller) 800x850 (something larger) These examples all have a larger height in order to account for the space of the button bar, menus, and status bar. Note that I did not do any work in the area of saving the size as a user preference. Miguel Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol app - size of start-up window
On Sep 12, 2008, at 4:12 PM, Robert Hanson wrote: There's help available for the command line, but to see it on a Windows machine you have to use java -jar jmol.jar -h not just jmol.jar -h In Jmol app on my MacBook Pro, each of these gives an error. java -jar jmol.jar -h usage: Jmol -o,--noconsole no console -- all output to sysout -q,--quality JPG image quality (1-100; default 75) or PNG image compression (0-9; default 2, maximum compres sion 9) -g,--geometrywindow width x height, e.g. -g500x500 when I type -g500x500 into the command line of Jmol, I get script compiler error: command expected. Same with -g 500x500 --geometry500x500 --geometry 500x500 What am I missing? Thanks, -Frieda -x,--exitexit after script (implicit with -n) -D property=value supported options are given below -b,--backgroundtransparent transparent background -c,--check check script syntax only -h,--helpgive this help page -i,--silent silent startup operation -l,--listlist commands during script execution -m,--menumenu file to use -n,--nodisplay no display (and also exit when done) -s,--script script file to execute -t,--threadedindependent commmand thread -w,--write CLIP or GIF|JPG|JPG64|PNG|PPM:filename For example: Jmol -ions myscript.spt -w JPEG:myfile.jpg output.txt The -D options are as follows (defaults in parathesis): cdk.debugging=[true|false] (false) cdk.debug.stdout=[true|false] (false) display.speed=[fps|ms] (ms) JmolConsole=[true|false] (true) jmol.logger.debug=[true|false] (false) jmol.logger.error=[true|false] (true) jmol.logger.fatal=[true|false] (true) jmol.logger.info=[true|false] (true) jmol.logger.logLevel=[true|false] (false) jmol.logger.warn=[true|false] (true) plugin.dir (unset) user.language=[CA|CS|DE|EN|ES|FR|NL|PT|TR] (EN) On Fri, Sep 12, 2008 at 3:05 PM, Reichsman Frieda [EMAIL PROTECTED] wrote: Hi, can someone remind me of how to tell the Jmol app to open its display window to a certain width and height? All I can find in the archives is the following post, which seems no longer to have an effect, and the scripting documentation is still unavailable (and I'm not too hopeful it would be in there)... Tim wrote: By the way is there a command-line option for adjusting the window size at start-up? No, but that is a very good idea. I just checked in code to allow one to set the window size on the Jmol application command-line: -g WIDTHxHEIGHT or --geometry WIDTHxHEIGHT Where WIDTHxHEIGHT is the width and the height in pixels separated by a lower case 'x' 500x550 (the current default) 300x350 (something smaller) 800x850 (something larger) These examples all have a larger height in order to account for the space of the button bar, menus, and status bar. Note that I did not do any work in the area of saving the size as a user preference. Miguel Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol app - size of start-up window
OK, I can open the Mac app Terminal easily enough and type the command in (just thought you had meant the Jmol command line). I'm assuming I have to get to the right directory and all that? Do I want to be in the same directory as the Jmol app? On Sep 12, 2008, at 4:32 PM, Robert Hanson wrote: Someone more familiar with Macs help me out here You need a terminal window and a prompt. At the prompt, on a PC at least, you type java -jar jmol.jar -h That starts the program and assumes that the path to java.exe is known to the system. If you can get that working, then you start Jmol using java -jar jmol.jar -g600x600 and you should be good to go. Bob On Fri, Sep 12, 2008 at 3:29 PM, Reichsman Frieda [EMAIL PROTECTED] wrote: On Sep 12, 2008, at 4:12 PM, Robert Hanson wrote: There's help available for the command line, but to see it on a Windows machine you have to use java -jar jmol.jar -h not just jmol.jar -h In Jmol app on my MacBook Pro, each of these gives an error. java -jar jmol.jar -h usage: Jmol -o,--noconsole no console -- all output to sysout -q,--quality JPG image quality (1-100; default 75) or PNG image compression (0-9; default 2, maximum compres sion 9) -g,--geometrywindow width x height, e.g. -g500x500 when I type -g500x500 into the command line of Jmol, I get script compiler error: command expected. Same with -g 500x500 --geometry500x500 --geometry 500x500 What am I missing? Thanks, -Frieda -x,--exitexit after script (implicit with -n) -D property=value supported options are given below -b,--backgroundtransparent transparent background -c,--check check script syntax only -h,--helpgive this help page -i,--silent silent startup operation -l,--listlist commands during script execution -m,--menumenu file to use -n,--nodisplay no display (and also exit when done) -s,--script script file to execute -t,--threadedindependent commmand thread -w,--write CLIP or GIF|JPG|JPG64|PNG|PPM:filename For example: Jmol -ions myscript.spt -w JPEG:myfile.jpg output.txt The -D options are as follows (defaults in parathesis): cdk.debugging=[true|false] (false) cdk.debug.stdout=[true|false] (false) display.speed=[fps|ms] (ms) JmolConsole=[true|false] (true) jmol.logger.debug=[true|false] (false) jmol.logger.error=[true|false] (true) jmol.logger.fatal=[true|false] (true) jmol.logger.info=[true|false] (true) jmol.logger.logLevel=[true|false] (false) jmol.logger.warn=[true|false] (true) plugin.dir (unset) user.language=[CA|CS|DE|EN|ES|FR|NL|PT|TR] (EN) On Fri, Sep 12, 2008 at 3:05 PM, Reichsman Frieda [EMAIL PROTECTED] wrote: Hi, can someone remind me of how to tell the Jmol app to open its display window to a certain width and height? All I can find in the archives is the following post, which seems no longer to have an effect, and the scripting documentation is still unavailable (and I'm not too hopeful it would be in there)... Tim wrote: By the way is there a command-line option for adjusting the window size at start-up? No, but that is a very good idea. I just checked in code to allow one to set the window size on the Jmol application command-line: -g WIDTHxHEIGHT or --geometry WIDTHxHEIGHT Where WIDTHxHEIGHT is the width and the height in pixels separated by a lower case 'x' 500x550 (the current default) 300x350 (something smaller) 800x850 (something larger) These examples all have a larger height in order to account for the space of the button bar, menus, and status bar. Note that I did not do any work in the area of saving the size as a user preference. Miguel Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people
Re: [Jmol-users] Jmol app - size of start-up window
OK, now I see I need to be in the same directory as the Jmol app. Done. The window size has changed, thank you for clarifying how to do this. Now - is there a command to change its starting location on screen, which currently places 90% of the window off my display? Gratefully, Frieda On Sep 12, 2008, at 4:32 PM, Robert Hanson wrote: Someone more familiar with Macs help me out here You need a terminal window and a prompt. At the prompt, on a PC at least, you type java -jar jmol.jar -h That starts the program and assumes that the path to java.exe is known to the system. If you can get that working, then you start Jmol using java -jar jmol.jar -g600x600 and you should be good to go. Bob On Fri, Sep 12, 2008 at 3:29 PM, Reichsman Frieda [EMAIL PROTECTED] wrote: On Sep 12, 2008, at 4:12 PM, Robert Hanson wrote: There's help available for the command line, but to see it on a Windows machine you have to use java -jar jmol.jar -h not just jmol.jar -h In Jmol app on my MacBook Pro, each of these gives an error. java -jar jmol.jar -h usage: Jmol -o,--noconsole no console -- all output to sysout -q,--quality JPG image quality (1-100; default 75) or PNG image compression (0-9; default 2, maximum compres sion 9) -g,--geometrywindow width x height, e.g. -g500x500 when I type -g500x500 into the command line of Jmol, I get script compiler error: command expected. Same with -g 500x500 --geometry500x500 --geometry 500x500 What am I missing? Thanks, -Frieda -x,--exitexit after script (implicit with -n) -D property=value supported options are given below -b,--backgroundtransparent transparent background -c,--check check script syntax only -h,--helpgive this help page -i,--silent silent startup operation -l,--listlist commands during script execution -m,--menumenu file to use -n,--nodisplay no display (and also exit when done) -s,--script script file to execute -t,--threadedindependent commmand thread -w,--write CLIP or GIF|JPG|JPG64|PNG|PPM:filename For example: Jmol -ions myscript.spt -w JPEG:myfile.jpg output.txt The -D options are as follows (defaults in parathesis): cdk.debugging=[true|false] (false) cdk.debug.stdout=[true|false] (false) display.speed=[fps|ms] (ms) JmolConsole=[true|false] (true) jmol.logger.debug=[true|false] (false) jmol.logger.error=[true|false] (true) jmol.logger.fatal=[true|false] (true) jmol.logger.info=[true|false] (true) jmol.logger.logLevel=[true|false] (false) jmol.logger.warn=[true|false] (true) plugin.dir (unset) user.language=[CA|CS|DE|EN|ES|FR|NL|PT|TR] (EN) On Fri, Sep 12, 2008 at 3:05 PM, Reichsman Frieda [EMAIL PROTECTED] wrote: Hi, can someone remind me of how to tell the Jmol app to open its display window to a certain width and height? All I can find in the archives is the following post, which seems no longer to have an effect, and the scripting documentation is still unavailable (and I'm not too hopeful it would be in there)... Tim wrote: By the way is there a command-line option for adjusting the window size at start-up? No, but that is a very good idea. I just checked in code to allow one to set the window size on the Jmol application command-line: -g WIDTHxHEIGHT or --geometry WIDTHxHEIGHT Where WIDTHxHEIGHT is the width and the height in pixels separated by a lower case 'x' 500x550 (the current default) 300x350 (something smaller) 800x850 (something larger) These examples all have a larger height in order to account for the space of the button bar, menus, and status bar. Note that I did not do any work in the area of saving the size as a user preference. Miguel Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College
Re: [Jmol-users] Jmol Tutorial-Authoring Template Released
On Sep 10, 2008, at 6:27 AM, Angel Herraez wrote: El 10 Sep 2008 a las 5:13, Robert Hanson escribió: http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/ contents /contents.htm Jmol Version 11.3.13 2007-08-28 16:07 really? I'm quite sure that tutorial was written some time ago, and does not use Eric's newest JTAT. So it's probably so, really. Thanks for pointing this out Bob. Yes, Angel is correct. The particular tutorial you've cited (Antibody) was finished well before JTAT was ready for use by others as a tutorial authoring tool. At that time, 11.3.13 was a current Jmol release. This is in contrast to the latest release of JTAT, a shell into which a tutorial can be built, and which has the current or nearly current Jmol. Here is a link to the empty shell -- no molecule loaded -- which has Jmol 11.6.RC12. http://www.bioinformatics.org/jmol-tutorials/jtat/template/contents/contents.htm This is what someone would download to start using JTAT to build a tutorial: Download JTAT We can of course update the Jmol version in previous JTATs, but obviously have not done that in this case (yet). Best, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Tutorial-Authoring Template Released
Forgot to mention, this is the best link for a demo of JTAT: http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo/contents/contents.htm Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // On Sep 10, 2008, at 6:27 AM, Angel Herraez wrote: El 10 Sep 2008 a las 5:13, Robert Hanson escribió: http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/ contents /contents.htm Jmol Version 11.3.13 2007-08-28 16:07 really? I'm quite sure that tutorial was written some time ago, and does not use Eric's newest JTAT. So it's probably so, really. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] identifying proteins in mol2 files
Hi Bob et al., If a mol2 file is correctly formated, should Jmol be able to recognize protein (as in 'select protein') and residue names? Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] identifying proteins in mol2 files
Some mol2 files contain amino acid residue names (preceded by the res number) at character 60 or 61, like this: 1 N 17.0470 14.0990 3.6250 N.3 1 THR 0.0677 2 CA 16.9670 12.7840 4.3380 C.3 1 THR 0.8095 3 C 15.6850 12.7550 5.1330 C.2 1 THR 0.4469 4 O 15.2680 13.8250 5.5940 O.2 1 THR -0.2562 5 CB 18.1700 12.7030 5.3370 C.3 1 THR 0.8346 6 OG119.3340 12.8290 4.4630 O.2 1 THR -0.1477 7 CG218.1500 11.5460 6.3040 C.3 1 THR 0.2847 So I thought perhaps there would be a way to recognize the structure with residue names as protein. Frieda On Sep 10, 2008, at 9:37 AM, Robert Hanson wrote: no. not that I know of. Only PDB and CIF support for that. Is there some sort of MOL2 designation that would suggest otherwise? On Wed, Sep 10, 2008 at 8:22 AM, Reichsman Frieda [EMAIL PROTECTED] wrote: Hi Bob et al., If a mol2 file is correctly formated, should Jmol be able to recognize protein (as in 'select protein') and residue names? Thanks, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] testing 11.6.RC8
Bob, 11.6.RC8 works fine for several of my web pages that use a variety of renderings, animations, echos, labels, centering commands, antialias toggle, spin, a looping script, and simple user-defined variables and functions. Fantastic! (...but not unexpected! :) Regarding syncing mouse gestures: sync across 2 applets using sync * on; sync * set syncMouse true works perfectly. The quaternion sync scheme that you suggested to me works perfectly in my amino acid comparison page, except for 2 amino acids. I am not sure what this means, but here are the details in case they are relevant: All the scripts that are called (for each amino acid) are the same except for the moveto command that initializes the position of each amino acid, and some definitions. I cannot see anything wrong with the moveto commands for these two amino acids, which work fine both when sync is not on, and when sync is on *without* the quaternion functions. With the quaternion commands invoked, these two amino acids take up anomalous positions that are translationally offset from where they should be, and they rotate around a point that is outside the amino acid, though their orientation is correct aside from that. The other difference of course is the coordinate files but I cannot see anything wrong when comparing these two mol2 files to the other amino acid files. If you want to look at this, the page is here: http://moleculesinmotion.com/aminoacids-sync/ and the amino acids that are not positioned correctly are arginine and histidine. (Note, some of the EPS values are not yet correct, please ignore). If it would be helpful I'd be happy to spell out what is in all the scripts, rather than you having to poke around; just didn't want to make this post even longer. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] testing 11.6.RC8
Thanks Rolf, this URL should work: http://permaculture.gaiahost.coop/moleculesinmotion/aminoacids-sync/ Frieda On Aug 22, 2008, at 9:19 AM, Rolf Huehne wrote: Reichsman Frieda wrote: If you want to look at this, the page is here: http://moleculesinmotion.com/aminoacids-sync/ and the amino acids that are not positioned correctly are arginine and histidine. (Note, some of the EPS values are not yet correct, please ignore). The page doesn't work on my system with Firefox 2.0.0.16 and Java 1.4.2_17 on Linux (and presumably also with firefox and Java =1.6.0_3 on any system) because of a Java security issue: FileManager opening http://moleculesinmotion.com/aminoacids-sync/scripts/start.spt script ERROR: io error reading http://moleculesinmotion.com/aminoacids-sync/scripts/start.spt: java.security.AccessControlException: access denied (java.net.SocketPermission 64.95.78.91:80 connect,resolve) eval ERROR: line 1 command 3 of file null: script scripts/start.spt Regards, Rolf - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a question about zoom
Hi Thomas, I think what you are looking for is fulfilled by the zoomto command. zoomto (atomset) 0 will bring the atomset to (approximately) occupy the applet display. I don't think this (the zero) is implemented for zoom, but I have not tried it. Also, zoomto has a timing parameter, so if you wanted the zoom to be instant, you could say zoomto 0 (atomset) 0 -the first zero is the time in seconds that the zoom will occur over, the second zero is the fit the atomset to the display setting. See the documentation for zoomto for more options. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // On Aug 19, 2008, at 2:34 PM, Thomas Stout wrote: Hi All -- I've been mucking about with zoom today and wondered this: is it expected behavior that the 100% level for zoom should be held constant for a loaded model? What I mean is this: when a structure is loaded, the 100% level is calculated by Jmol to be the factor at which all atoms are completely visible on the screen through all rotations using the default vanderWaals rendering percentage. If I then issue zoom 200, the display is zoomed in by 200 percent -- expected behavior. If, however, I issue: zoom (atom expression) 100 (for example, zoom (*:B) 100), would it not be reasonable to expect the display to be altered such that the stated atom expression is now scaled to (approximately) fit the Jmol display? I'd like to use this to automatically transition to selected portions of PDB files (such as ligands or amino acid ranges of interest) and have the proper display zoom auto-calculated. Is there another way to do this? Can I calculate on the fly a boundbox for the current selection and set the zoom level to fill the display with this new boundbox? Cheers, Tom - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] mol2 files
Hi Bob, I have some mol2 files wherein Jmol cannot read the embedded EPS (or are they more correctly called partial charge) values, and also Jmol fails to render one atom in the file. An example file is attached, along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't read EPS) and ala.mol2 (Jmol does read EPS), Comparing the two mol2 files, the format is slightly different. I am not sure if the file is formatted incorrectly (generated by the program AtomSmith), or if Jmol is too strict. The differences are as follows. In the ala-problem.mol2 file, 1. The eps values from are offset by one additional space from the coordinates, and 2. the three-letter abbreviation for the amino acid is missing in each row from inbetween the number 1 and the EPS values. When I change both these aspects to mimic the file ala.mol2, Jmol can read the eps values. 3. In the ala-problem.mol2 file I also had to remove the ALA that appears as characters 4, 5 and 6 in the line for atom #1, in order for Jmol to be able to render that particular atom. Frieda ala-problem.mol2 Description: Binary data ala.mol2 Description: Binary data // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] mol2 files
I wrote: and also Jmol fails to render one atom in the file. this only occurs after I fix problems 1 and 2 (as listed in previous post). // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] mol2 files
They come from AtomSmith, which is from Bitwixt software. The file that works in Jmol is included with the program; the file that does not work in Jmol is AtomSmith's output when it starts with a pdb file, puts an EP surface around it, and exports it as mol2. If it's their formatting needs changing, then I can urge them to deal with it - I have already emailed them about it twice. Frieda On Aug 14, 2008, at 2:19 PM, Bob Hanson wrote: Where do these files come from? The mol2 format does not allow for anything between the number and the element symbol on that atom line. http://www.tripos.com/tripos_resources/fileroot/mol2_format_Dec07.pdf Bob Reichsman Frieda wrote: Hi Bob, I have some mol2 files wherein Jmol cannot read the embedded EPS (or are they more correctly called partial charge) values, and also Jmol fails to render one atom in the file. An example file is attached, along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't read EPS) and ala.mol2 (Jmol does read EPS), Comparing the two mol2 files, the format is slightly different. I am not sure if the file is formatted incorrectly (generated by the program AtomSmith), or if Jmol is too strict. The differences are as follows. In the ala-problem.mol2 file, 1. The eps values from are offset by one additional space from the coordinates, and 2. the three-letter abbreviation for the amino acid is missing in each row from inbetween the number 1 and the EPS values. When I change both these aspects to mimic the file ala.mol2, Jmol can read the eps values. 3. In the ala-problem.mol2 file I also had to remove the ALA that appears as characters 4, 5 and 6 in the line for atom #1, in order for Jmol to be able to render that particular atom. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] just for fun ;)
Excellent Bob! And quite the final touch! Frieda On Aug 11, 2008, at 10:12 PM, Bob Hanson wrote: OK, just for fun... http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm click the long red link. SOMEONE's going to have some fun with this. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] just for fun ;)
Lemme at it!! ;) On Aug 12, 2008, at 9:37 AM, Bob Hanson wrote: OK, I'm expecting you to do incredible things with this, Frieda. Bob Reichsman Frieda wrote: Excellent Bob! And quite the final touch! Frieda On Aug 11, 2008, at 10:12 PM, Bob Hanson wrote: OK, just for fun... http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm click the long red link. SOMEONE's going to have some fun with this. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jvxl pdf unavailable
Hi Bob, Your JVXL format pdf file is apparently not available right now at this URL: http://www.stolaf.edu/people/hansonr/jmol/docs/JVXL-format.pdf The connection times out in Safari3/Mac, and in FF2/Mac, never gets past starting... Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] electrostatic potential surface coloring
Thank you again, Bob, for your help. The trick is to use Jmol's
calculated values for surface MEP as the defining points for the
coloring scale, and not the partial charges values in the coordinate
file. (Maybe not so much of a trick if I knew what I was doing to
start with!) These values appear in the console when you set
debugscript on, which is very handy Bob!
I have posted a page with a grid for comparing the results of
... color range all ... with ... color range [defined] ...
and
calculating the MEP over the side chain only vs. calculating for the
whole amino acid., i.e., the option including select {*} that Bob
outlines below.
http://moleculesinmotion.com/patterson_aas2/aminoacids/index.htm
The isosurface command used is listed above each column, and the data
calculated by Jmol are listed in a table below the applets. I hope
this may be useful to others pondering some of the options for MEP
display.
To me, for teaching about polar and non-polar side chains, calculating
over the side chain alone looks like the way to go, and restricting
the color range creates a very non-polar looking surface for valine,
contrasting with a nice charge level for asp. I am not sure I can
figure out what is going on with valine with 'color range all' and
calculating only over the side chain. (Top row, third column).
I'll be using this to make a page that will enable students to compare
the MEP of any two amino acid side chains and hopefully also
nucleotide bases and a few other small molecules. When it's finished I
will post the URL to the list, hope it may be of interest to some for
teaching purposes.
Best,
Frieda
On Aug 6, 2008, at 2:25 AM, Bob Hanson wrote:
I think you want
isosurface select {} molecular map select {*} mep
That is, when you run the mep, you want to indicate that for THAT part
of the calculation, you want all atoms selected. I hadn't realized
myself that two selects work here -- I suppose it could be useful.
Or not.
//
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//
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Re: [Jmol-users] electrostatic potential surface coloring
Thanks Bob. If I understand correctly, this means that Jmol is calculating the surface MEP based on the values in the file, which do not represent absolute MEP but rather, are partial charges. And that means that when Jmol calculates the surface MEP for only part of the amino acid (the side chain), the absence of the 'backbone' atoms greatly influences the calculation of the potential over the side chain, yes? And so the absence of those atoms is creating the effect I'm seeing of diminishing the potential on the charged side chain, and magnifying it a bit on the uncharged side chain? This leads to another question, would it be possible to show a partial surface? That is, 'build' the surface for the entire amino acid, but only display only the surface over the side chain. I imagine this would be a feature request, would it be feasible to do this? Frieda On Aug 5, 2008, at 12:11 PM, Bob Hanson wrote: if you are mapping MEP data, remember that a MEP calculation is being done that converts charge on atoms to potential at some distance (on the surface) from a bunch of atoms, collectively. This value falls off with distance. So that's probably why your numbers are low. They aren't just charges, and really they are just approximations of electron potential, as well. If you want to map the charges themselves, you will need to use map property partialcharge. But that will look somewhat blotchy, I suspsect. I'm sure you have the color range/absolute business correct. Bob Am I misunderstanding what color range/absolute x.xxx y.yyy should be doing? Is there a way to get the coloring for color range all but only show the surface for the side chains? Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] electrostatic potential surface coloring
Hi All, I am trying to render the electrostatic potential surfaces for the 20 individual amino acids, to illustrate the differences in side chain polarity. (Ultimately, I will be showing partial surfaces, over the side chains only.) I have some mol2 files of zwitterionic amino acids containing the EPS values. The highest EPS value in each file is 0.2751 and the lowest is -0.6478 (or -0.6464, which I take to be a negligible difference). These values are for the charged amines and carboxyls, and my thought was that they would set a good absolute scale for showing the differences in polarity between the side chains. (This will be particularly important when I render the isosurface over the side chains only, otherwise I will get relative coloring that will make the nonpolar side chains look similar to polar side chains.) Using a red- white-blue color scheme, then, I expect that nonpolar side chains such as valine should come out with very faint red and blue, whereas charged side chains such as aspartate should have significantly deeper colorings. When I use the command isosurface colorscheme rwb sasurface 0.1 color range all map mep the results make perfect sense if I am looking at the surface of the entire amino acid, but once I restrict it to the side chain, the relative coloring I don't want (as above) is the result. So to force the range to be absolute, I am using the command isosurface colorscheme rwb sasurface 0.1 color range -0.6478 0.2751 map mep Because these are the highest and lowest values in the files, I'd expect the charged groups to show up as bright red or blue, and nonpolar areas to be faint. However, I am not getting the results I am anticipating. Aspartate's surface has only faint colors, and valine is actually a medium shade of blue. I don't get it. In response to the command above, Jmol comes back with this for Asp: color range -0.6478 0.2751; mapped data range -0.26758346 to 0.03863874 and this for Val: color range -0.6478 0.2751; mapped data range -0.19274539 to 0.16532882 What does the mapped data range refer to? The numbers seem to correspond with the colors I am seeing, but do not correspond to the eps values in the file. I've also tried using ... color absolute -0.6478 0.2751 ..., which seems to give the same effect. I've tried using fewer decimal places, and experimented with different absolute ranges, but I don't want to choose something arbitrary. Am I misunderstanding what color range/absolute x.xxx y.yyy should be doing? Is there a way to get the coloring for color range all but only show the surface for the side chains? Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] coordinate files for DNA base tautomers
Hi all, Anyone know of existing coordinate files for tautomers of the DNA bases? Have searched several of the usual databases, etc., with no luck. So before I make some, just thought I'd check if anyone has them. Thanks, Frieda /// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: Protein Explorer
Looking great Bob. This is a fantastic achievement! Here is some feedback on functions: Safari 3.1.2 Mac OS 10.5.4 Using 1d66 --- FirstView --- - Chains are all the same color instead of each chain a different color - Click on an atom - report in message window is delayed until the mouse moves (status bar of browser shows info immediately). It would be even nicer if the report showed up in the structure window as an echo, something that was not possible with Chime. (Are you ready for suggestions or just looking for testing at this time?) - Spin speed is very fast, recommend a slower default speed (eg, 5) - The little axes in the corner are cool! and handy. QuickViews - tested almost all views, with All selected. - Color Chain (PE) is not working - colors all cahins cyan, unless used immediately following Color Chain (Chime), in which case it does not change the color. - Color pur/pyr - not working, no change in color. - Hbonds- not working, no effect - Surface- not working, got a popup window with The requested URL /pe/ protexpl/htm/h_slow1.htm was not found on this server. - Hide- as with Chime, checkboxes work when checked but not when unchecked. But with Jmol I would think it is possible to make them work when unchecking. - Seq3D- working for clicking to show protein residues, but not DNA bases. Send feature - Awesomely cool feature! - worked fine in test mode - emailed html file did not load the structure :( - link to open in JmolPE worked perfectly :) That's all I had time to test now. HTH, Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // On Jul 17, 2008, at 11:24 AM, Bob Hanson wrote: Eric, and others. Jmol Protein Explorer is ready for testing and may be considered in beta state. http://chemapps.stolaf.edu/pe or Jmol.ProteinExplorer.org It is based on Protein Explorer and has the same look and feel. Many new capabilities (for example, sending live snapshots to one's self or a colleague via Email, animation buttons, biomolecules, crystallographic symmetry, etc.), some of which are implemented from Jmol itself; some from PE-based pages. Help pages are still in the process of being transferred to a database; some references there are still to the Chime version. Bob Eric Martz wrote: Dear Dan, At this point there are so many problems with Chime, and consequently with PE, that I am reluctant to invest any more time working on PE-Chime. Involving Chime SP7 will very likely open a Pandora's box of complex and time-consuming Internet Explorer 7 issues. Someday I hope to port PE to Jmol, which will avoid all these problems, but that is a major project and the starting date, much less the completion date, is uncertain. Meanwhile, I am investing my time in Jmol-based and other resources that are truly cross-platform and avoid most of the browser-specific issues, notably the technologies summarized at http://top5.molviz.org http://top5.molviz.org/Hopefully you will find that these resources meet your needs, perhaps better than PE. Most of them are even easier to use than PE. I have taught one-day courses to researchers recently in the USA, Israel, and Japan ( http://workshops.moviz.org http://workshops.moviz.org/). I don't even mention PE in these courses, yet the researchers feel empowered to do everything they need. (Would you like one of these courses at JHU? I got my Ph.D. at JHU Homewood!) If there are specific tasks of interest, please ask, and I'll be happy to recommend solutions if known to me. Sincerely, -Eric *From: *Dan Raben [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Date: *July 9, 2008 2:26:53 PM EDT *To: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Subject: Protein Explorer * Are there any plans to upgrade PE to use Chime 2.6 _SP7? _ This has been out for almost a year I believe and I’m wondering if PE is going to stick with Chime 2.6 _SP6_. Thanks…DMR Daniel M. Raben, Ph.D. Professor The Johns Hopkins University Department of Biological Chemistry 725 North Wolfe St. Baltimore, MD 21205 Tele: 410-955-1289 Fax: 410-614-8729 Email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org http://top5.molviz.org/3D Wiki with Scene-Authoring Tools http://Proteopedia.Org http://proteopedia.org/Biochem 3D Education Resources http://MolviZ.org http://molviz.org/See 3D Molecules, Install Nothing! - http://firstglance.jmol.org http://firstglance.jmol.org/Protein Explorer - 3D Visualization: http://proteinexplorer.org http://proteinexplorer.org/Workshops: http://workshops.proteinexplorer.org
