Begin forwarded message:
From: Elaine Meng <meng@cgl.ucsf.edu> Date: Wed Mar 23, 2005 9:39:41 AM US/Pacific To: Grant Jacobs <gjacobs@bioinfotools.com> Subject: Re: [Chimera-users] Zones to create inspector list of "contacts"
Hi Grant, You can write out the contents of the current selection with Actions... Write. More details can be viewed at: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#writespec
However, the resulting text file will simply list all selection contents (i.e., not in pairs of what is contacting what). I don't know if that is sufficient for your purposes.
If you are specifically looking at H-bond interactions, however, FindHBond includes an option to write out all the H-bonded atom pairs and the distances between them. Man pages: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ findhbond.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html
Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Wednesday, March 23, 2005, at 02:55 AM, Grant Jacobs wrote:
I am trying to achieve something with this effect:
Generate a list of all the atoms in other molecules of a multi-protein complex that are within a specific "contact" distance of atoms a molecule of interest in the complex, with them presented in the same way that H-honds or distances are illustrated.
You can use Select:Zones to get the atoms that lie within a set distance of a molecule. All that seems to be needed is for the Select:Zones operation to optionally generate a list of atom pairs that the inspection things present.
So far I can't seem a simple way of doing this without hacking code or doing it manually. Is there a way of doing this currently, or should this be looked at as future possible feature?
Obviously, there are other useful "neighbour" operations you can do also, e.g. neighbours within the current selected molecule, neighbours by atom/residue type.
Grant