[chimera-dev] Accessing rotation matrix of molecule models

Eric Pettersen pett at cgl.ucsf.edu
Fri Jul 19 10:40:08 PDT 2002

The one thing I would add, and you may know this already, is that if you 
have atom1 and atom2 in Python and want the distance between them after 
transformation, you do:



On Thursday, July 18, 2002, at 05:47 PM, Greg Couch wrote:

> On Thu, 18 Jul 2002, Thomas Goddard wrote:
>>   When you get atom coordinates with atom.coord() you get the original
>> xyz values from say a PDB file.  The m.openState.xform applied to those
>> coordinates gives you the displayed xyz Chimera coordinates of the atom
>> taking into account the rotation and translation.  So you should apply
>> the xform before comparing distances between atoms in different molecules.
> Use atom.xformCoord() to get the transformed coordinate.  Same thing,
> but the transformation is done in C++ instead of Python.
> 	Greg
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

More information about the Chimera-dev mailing list