[chimera-dev] Using chimera.BondRot

Eric Pettersen pett at cgl.ucsf.edu
Thu Apr 16 12:16:37 PDT 2009

Hi Fred,
	Since the 1.3 release I have put some effort into making it possible  
to create/drive dihedrals from a Chimera command.  That work isn't  
entirely completed (the command doesn't exist yet) but enough of the  
work has been done to help you out.  In particular, there is a  
BondRotMgr module and the StructureMeasure dialog will only respond to  
torsions created using the BondRotMgr API.  So, if you create a  
torsion directly with chimera.BondRot the dialog won't pop up anymore  
-- which is what you want.  Remember to destroy the BondRot instance  
once you are done adjusting the torsion (with BondRot's destroy()  
	You need to use a daily build to use the new functionality.  It will  
also be included in the next production release.

                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Apr 16, 2009, at 11:06 AM, Frederic RODRIGUEZ wrote:

> Dear Chimera developers
> We want to generate structures (ligand+protein) in which
> we impose a variation (0 to 360 degrees, with step of 1 or
> 5, 10 degrees) of one or two dihedrals of the ligand.
> We want to use Chimera to select interactively, a list of
> dihedrals, and launch a script which do the rotations, produce
> PDB structures, save them. After we want to do another
> processing but using our own code (and perhaps including
> a new extension GUI, python, we work under Windows XP).
> We want to use BondRot functions, so we have explored module
> StructMeasure (and other related files ... BondObject.h) in
> order to understand how we can use this feature.
> We have done some experiments using a modified version
> of this extension so that we can select and rotate dihedrals
> as we want.
> If we make a script or a new extension, and let original StructMeasure
> module in place, we have problems. When we add a bond rotation using
> an expression such as: br = chimera.BondRot(bond) the panel  
> AdjustTorsions
> of StructMeasure is always loaded.
> We would like to know if we can do our task without the use of
> chimera.BondRot , or if we can use it independently of
> StructMeasure dialog.
> thanks,
> Fred Rodriguez, Mansi Trivedi
> -- 
> Frédéric Rodriguez
> Laboratoire de Synthèse et Physicochimie
> de Molécules d'Intérêt Biologique
> UMR 5068 CNRS / Université Paul Sabatier
> 118 Route de Narbonne
> 31062 TOULOUSE cedex 9, France
> vce: - fax: 33 (0)
> elm: build at chimie.ups-tlse.fr
> _______________________________________________
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> Chimera-dev at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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