[Chimera-users] torsion angles to x,y,z coordinate

Chinh Su Tran To chinh.sutranto at gmail.com
Fri Mar 22 19:14:57 PDT 2013

Thanks Elaine. I'll have to script it because I have 10 torsions (for each
of the 100 ligands) to change. Those 10 are generated from a GA program. I
need to use the "rotation" command as you suggested. Do I have to WritePDB
for every change of torsions to get the new conformation (new x,y,z
coordinates) 'cause I need the new conformations to do DOCK for the next

Dear Eric,
My molecule is a drug (a small molecule). It is not a protein. I was
wondering if changing that amount of torsions is too much. We're trying to
do some optimizations using GA instead of running MD.

Thank you and hope get more your advice.


On Saturday, March 23, 2013, Eric Pettersen wrote:

> On Mar 22, 2013, at 10:51 AM, Elaine Meng wrote:
> Hi Chinh,
> You can change torsion angles using the Adjust Torsions GUI (in menu under
> Tools... Structure Editing)
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust
> >
> ... or the rotation command
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html>
> If you have lots of values, you would probably want to script it, but it
> probably wouldn't be that easy/convenient since the commands (or python, if
> you do a python script) will need to specify the 4 atoms used to define
> each torsion.
> What Elaine says is absolutely correct.  What I would add though is that
> if the torsions you are changing are the phi, psi, or chi angles of
> standard amino acids, then adjusting them is somewhat easier since they are
> attributes of the residue and setting the attribute will change the
> torsion.  For example, to change the phi angle of residue 14.A to 90
> degrees:
> setattr r phi 90 :14.a
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
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