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() method). You need to use a daily build to use the new functionality. It will also be included in the next production release. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu 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: 05.61.55.85.66 - fax: 33 (0)5.61.55.60.11 elm: build@chimie.ups-tlse.fr
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