[Chimera-users] distance measurements

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 31 09:07:22 PDT 2009

Hi Jean-Paul,
The possibilities I have in mind are not particularly "automatic":

(a) use multiple "distance" commands, each specifying a pair of  
atoms.  You would probably want to write a script in your favorite  
language to create the Chimera command file with all those distance  

(b) use the "findclash" command (or GUI) with an extremely lenient  
cutoff (large negative overlap), which will report all the distances  
within that cutoff.  Specify finding interactions between your one  
residue and all other atoms to get the distances and overlaps for all  
atom-atom pairs meeting the criteria.

With (b) you would get a lot of output to sift through.  If you wanted  
only certain atoms, for example CA-CA distances only, you would either  
just use approach (a) or use (b) with postprocessing to extract only  
the lines of interest.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 31, 2009, at 5:17 AM, Jean-Paul Armache wrote:

> hello,
> i would like to ask whether there is a way of automatically  
> measuring the distance from all residues in a chain
> to residue X in the same chain?
> best regards,
> jean-paul armache

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