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

Elaine Meng meng at cgl.ucsf.edu
Sat Mar 23 11:17:06 PDT 2013


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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