I would like to do the following task:


I have three complexes of three different ligands with the same enzyme  and I would like to rotate/translate  the electron density maps of two of these complexes in order to superpose them onto the first complex.  I need to do the superposition based on the coordinates of the ligands and not on the common enzyme residues since there are conformational changes that differ in the three complexes. I can nicely superpose the ligands using Pymol “Pair fitting” wizard but then my questions are:


1-Is it possible to output  to the console the superposition matrix after pair fitting ?


2- Is it possible to apply these transformation matrices to mesh objects (from electron density maps)?







Carlos Martinez Fleites

Structural Biology Laboratory

Department of Chemistry

The University of York


York YO10 5YW

United Kingdom


Tel:        +44 1904 328278

Fax:      +44 1904 328266

E-mail: martinez@ysbl.york.ac.uk