[Chimera-users] Adjust torsion and bump checking

Eric Pettersen 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.

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 Pettersen
                         UCSF Computer Graphics Lab

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