[Chimera-users] [chimera-dev] clashes and contacts with hidden models

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 28 09:21:30 PST 2011

On Feb 28, 2011, at 5:28 AM, Elisabeth Ortega wrote:
> I have a question related to the calculation of the clashes between two (or more) models. What I have to do to count only the clashes of the Active or Displayed models? I mean, if I have 3 models in the model panel and I only want to calculate the clashes between the models 1 and 2 without close the model 3, what I have to do? 
Hi Elisabeth,
With either the graphical interface of Find Clashes/Contacts or the command findclash, you can specify which two groups of atoms to examine for clashes.  The remaining atoms will be ignored. I believe it doesn't matter whether the atoms are displayed or active.  With the command, it would be something like

findclash #1 test #2 [other options]

Another example:
findclash ligand overlap -0.4 hb 0 test aromatic

Use command "help findclash" to see the manual page, or view it here:

With the GUI, the procedure is slightly different: you would select one group (say #1), click Designate, choose option "second set of designated atoms", select the second group (say #2), click "Designate selection as second set", Apply.  Click the Help button to see the manual page, or view it here:

This is more of a chimera-users at cgl.ucsf.edu question (how to use Chimera) than chimera-dev (programming related to Chimera), so I'm also CC-ing the former list.

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

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