[Chimera-users] Adjust torsion and bump checking

Kim, Sunghoon sunghoon.kim at Vanderbilt.Edu
Tue May 4 10:56:50 PDT 2010

Hi all,

I would like to do the bump checking for the various rotameric states of a specific side chain generated by the rotation about dihedral angles. Bumps were detected by chimera command 'rotation' and 'findclash' and at first the script seemed working OK, but I'm not sure if the chi angles were correctly defined. When we look at the 'clashes/contacts' panel in Chimera, there are atom options for "Near" and "Far" positions in the rotating bonds. How can I specifying the 'Near' and 'Far' atoms in my 'rotation' command line in my python script to define my chi angles ?

Thanks in advance for any info that you can provide.

Sunghoon Kim
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