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

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?

[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

Re: [Jmol-users] Jmol app - size of start-up window

, 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

Re: [Jmol-users] Jmol app - size of start-up window

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

Re: [Jmol-users] Jmol app - size of start-up window

. 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

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,

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

[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

Re: [Jmol-users] identifying proteins in mol2 files

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

[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

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

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

[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)

[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

Re: [Jmol-users] mol2 files

. 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

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

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

[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

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

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

[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

[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

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