[PyMOL] Fitting/alignment of non-identical sequences

[Robert C. <rl...@po...>]

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.                         <rl...@po...>
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