Dear Folks, I know a number of people have stumbled over the difficulty of calculating RMSD values for structures of non-identical sequences. While teaching a class that introduced students to the use of PyMOL to look at protein structures and to the study of certain structurally homologous structures, I struggled with the difficulty of explaining how to do this. In the end, I wrote a couple of new web pages introducing PyMOL and the process of aligning structures. You can visit these at:
http://adelie.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol http://adelie.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment (these are now linked from my PyMOL scripts page as well). The second of these shows how one can calculate the backbone RMSD for a selection by changing all the residues to glycines and resetting the residue numbers to be the same in the two structures. After playing around with this I finally got tired of doing it manually, so of course I wrote a python script to do this. It uses the alter command (so it isn't fast!) to modify the alt, name, resn, resi, chain, and segi values to match in the two sets. Then it calculates the RMSD using the fit command and then resets everything back the way it was. It also creates two new objects showing the backbone (or C-alpha) atoms that were using in the match. This script (fitting.py) is available in my script repository: http://adelie.biochem.queensu.ca/~rlc/work/pymol Feedback is welcome as always! Cheers, Rob -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
