[Chimera-users] Distance between atoms using Python

Tom Goddard goddard at cgl.ucsf.edu
Fri Jul 18 10:39:41 PDT 2008

Hi Ed,

  Attached is some Python code for controlling ligand display based on 
distance between two atoms.


Edward Brignole wrote:
> Tom,
> Thanks again for your help with that atom display.  Got another 
> MDtrajectory issue for you.  I've got a ligand in each of 10 domains 
> in the structure and I only want to display the ligands in the frames 
> that have less than a certain distance between a particular atom in 
> the ligand and a particular atom in a neighboring domain.
> The distance command won't work for me because all it does is add a 
> distance to the distance dialog when I need it as a variable in the 
> script to evaluate with "if distance < 10: display atomspecs"
> Sorry to keep bugging you with these things but I assure you it isn't 
> without trying for several hours to no avail before finally resorting 
> to asking.
> Ed

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