[Chimera-users] Detection of sterical clashes within selection

James Starlight jmsstarlight at gmail.com
Mon Nov 10 07:03:15 PST 2014

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,

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