Re: [chimera-dev] Accessing rotation matrix of molecule models

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