Fwd: [Chimera-users] Zones to create inspector list of "contacts"

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 23 09:41:27 PST 2005

Begin forwarded message:

> From: Elaine Meng <meng at cgl.ucsf.edu>
> Date: Wed Mar 23, 2005  9:39:41 AM US/Pacific
> To: Grant Jacobs <gjacobs at 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 at 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

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