On May 4, 2010, at 10:56 AM, Kim, Sunghoon wrote:

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.

Hi Sunghoon, 'rotation' is a generic command and doesn't know anything specific about chi angles, phi/psi angles, etc. It simply changes the angle by the amount you specify from its current position. So if you want a chi angle of 180, "rotation 180" about the appropriate bond won't get you there -- it will simply turn that bond by 180 degrees from where it started. However, in recent versions of Chimera Residues have phi/psi/chi attributes. Therefore the easy way to set the chi1 angle of a residue to 180 in a Python script would be: r.chi1 = 180 the equivalent Chimera command is: setattr r chi1 180 #0:<residue you want> I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu