Re: [Jmol-users] delete hydrogens minimize addHydrogens

2010-02-16 Thread Robert Hanson
OK, Otis. We are making progress. With this next revision, imines should work, and there is the possibility that cumulenes will work. The qualification is that if the starting cumulene has no hydrogens at all (for example, just C=C=C), Jmol won't be able to handle it, because it adds the H atoms

[Jmol-users] selected and save pdb of specific hetero nonaqueous HETATM ( hetero and not water) in a protein complex PDB

2010-02-16 Thread albertasson
Dear users, I am looking on a way or something that allows saving only the PDB coordinates of the all hetero atoms in protein complex from protein data bank. I can visualize all these hetero atoms and save the picture, but I cannot save the PDB. When I try to do it, I receive the complete protein

Re: [Jmol-users] selected and save pdb of specific hetero nonaqueous HETATM ( hetero and not water) in a protein complex PDB

2010-02-16 Thread Angel Herráez
Hi Albertsson Using a script: http://chemapps.stolaf.edu/jmol/docs/#writemodel says only selected atoms are saved From the popup menu, I think you can only do this in MOL format: Show Extract MOL data -- SOLARIS 10

Re: [Jmol-users] Fwd: auto-orientation?

2010-02-16 Thread Rolf Huehne
Thomas, I am gladI could help you and I don't have any objections to both proposals. Regards, Rolf Thomas Stout schrieb: Rolf -- I have now had a chance to locally implement your approach to this question of optimal orientation. What you have done is exactly what I wanted was

Re: [Jmol-users] Fwd: auto-orientation?

2010-02-16 Thread Angel Herráez
Can you define more precisely what is you are doing to position according to the boundbox? Jmol has, since ancient times, commands to orient according to Top, Bottom, etc, which I'd say are related to the boundbox. In fact, I've never seen much advantage in having them in the menus for

Re: [Jmol-users] auto-orientation?

2010-02-16 Thread Thomas Stout
To follow up on my question from last week concerning auto-orientation, Rolf Huehne very graciously pointed me in the direction of a solution that he had already crafted for JenaLib. He uses the dimensions of the bounding box, selected for the atoms of interest, and arrays the longest two vectors

Re: [Jmol-users] auto-orientation?

2010-02-16 Thread rgb
On Tue, 16 Feb 2010 12:04:32 -0800, Thomas Stout thomasjst...@gmail.com wrote: To follow up on my question from last week concerning auto-orientation, Rolf Huehne very graciously pointed me in the direction of a solution that he had already crafted for JenaLib. He uses the dimensions of the

Re: [Jmol-users] auto-orientation?

2010-02-16 Thread Rolf Huehne
r...@ellerbach.com schrieb: On Tue, 16 Feb 2010 12:04:32 -0800, Thomas Stout thomasjst...@gmail.com wrote: To follow up on my question from last week concerning auto-orientation, Rolf Huehne very graciously pointed me in the direction of a solution that he had already crafted for JenaLib.

Re: [Jmol-users] auto-orientation?

2010-02-16 Thread Thomas Stout
I am doing the same: all atoms in the unique asymmetric unit - sans solvent - are considered to be the atoms of interest on file loading (even though in the background I am loading with the packed cell). I have a second implementation of orient on the GUI that takes and utilizes the current

[Jmol-users] Get an Atom Property by Index

2010-02-16 Thread Otis Rothenberger
Hello- I have been getting atom properties by atom number: e.g. document.getElementById(appletID).getPropertyAsString(atomInfo[1].color) I am working with some script issues that force me to get atom properties by atomIndex. Is there any way to use atomIndex as the atomInfo array index? I've