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

[Chinh Su Tran To]

thank you Elaine.

On Sunday, March 24, 2013, Elaine Meng wrote:

> Hi Chinh,
> If you want a PDB file for each conformation, yes, you would have to use
> Write PDB (or command "write").
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
>
> Theoretically no number of rotations is too many.  We just meant it would
> probably be too many to type in each command yourself.  Instead you would
> prefer to script it in either Chimera commands or python, as mentioned in
> my previous message.
> Elaine
>
> On Mar 22, 2013, at 7:14 PM, Chinh Su Tran To wrote:
>
> > 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 step?
> >
> > 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.
> >
> > Regards,
> > Chinh
> >
> > 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
> >
>
>
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