[Chimera-users] Adjust torsion and bump checking
pett at cgl.ucsf.edu
Tue May 4 15:29:37 PDT 2010
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.
'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
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.
UCSF Computer Graphics Lab
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