Re: [Jmol-users] Jmol Tutorial-Authoring Template Released

http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/contents/contents.htm Jmol Version 11.3.13 2007-08-28 16:07 really? Bob On Mon, Sep 8, 2008 at 10:15 PM, Eric Martz [EMAIL PROTECTED]wrote: At long last, I have completed a version of the Jmol Tutorial-Authoring Template (JTAT)

Re: [Jmol-users] Jmol Tutorial-Authoring Template Released

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

Re: [Jmol-users] Placing Jmol image in same web page

Steven R. Spilatro wrote: Hi everyone, I've created a demo page for placing images of the Jmol model into the same web page, drawing upon some ideas and code from Angel Herráez and Dean Edwards. For compliant browsers, the base64-encoded Jmol image is simply directly to an image

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

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

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

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

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 [...]

[Jmol-users] Placing Jmol image in same web page

Thanks to everyone for the feedback on the 'Placing Jmol image in same web page' which I've updated. http://www.marietta.edu/~spilatrs/MnQuiry/JmolDemo/jmolImgCopy.html 'Output size' now shows a default (Lesson of the Night: do not put radio buttons in a table if you want to set the checked

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

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

Re: [Jmol-users] Placing Jmol image in same web page

On Wed, Sep 10, 2008 at 9:33 AM, Steven R. Spilatro [EMAIL PROTECTED]wrote: Thanks to everyone for the feedback on the 'Placing Jmol image in same web page' which I've updated.