[Chimera-users] Calculate distances between ligand atoms to select the most distant pair

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 4 09:39:23 PST 2016


Hi,
Not sure I exactly understand the question, but I’ll try to answer anyway.

If you use command “measure distance” with two sets of atoms it will report the minimum of all the pairwise distances.  However, I don’t know of any way to get the maximum of all the pairwise distances other than doing all the pairwise measurements individually.  Everything can be done with a python script, but somebody else would have to advise on that.

Example for getting minimum distance between ligand and residue 255 of pdb 2gbp, commands:

open 2gbp
measure distance ligand :255

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance>

Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 3, 2016, at 6:49 PM, Felipe Vasquez <anfelvas at gmail.com> wrote:

> Hi,
> I am interested in select those two atoms more distant into a ligand. However, how could I estimate this so I have not to calculate the distance manually for all possible pairs one by one? 
> Thanks in advance for your help.
> Be



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