[Chimera-users] Detection of sterical clashes within selection

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 10 09:46:02 PST 2014


Hi James,
Take a look at the "findclash" command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

For example, if you had selected the lipids, maybe something like:

findclash protein test sel 

That would look only between protein and lipids.  If you wanted to find all clashes including protein-protein and lipid-lipid, you could select both protein and lipids, and then use a command something like:

findclash sel test self

It could be done a few different ways like using atomspecs instead of selection.  I recommend looking at the command options because there are also adjustable parameters, and choices as to how to show the results (lines, coloring, etc.).  The command has all the same features as the GUI tool Find Clashes/Contacts (in menu under Tools… Structure Analysis).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

I hope this helps,
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 Nov 10, 2014, at 7:03 AM, James Starlight <jmsstarlight at gmail.com> wrote:

> Dear Chimera users!
> 
> This timeI'm writing of some automatic script aimed on the embedding of the receptors into the membrane consisted of the pre-equilibrated lipids as well as hole for the protein. The main issue that some of the receptors consist of the bulky PHE or TRP side chains on their surface which are overlap with the lipids atoms.  As the result subsequent MD simulation of these systems is crushed although of long minimization stage prior to it.  I'll be very thankful if someone provide me with some Chimera's command for automatic detection of these steric clashes (overlapped atoms) for a given selection (e.g protein and lipids) based on which I'll be able to write automatic python script. 
> 
> Thanks for help,
> 
> James




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