Dear Folks, * I <r...@post.queensu.ca> [2005-03-29 16:27] wrote: > 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:
It occurred to me <sound of palm smacking forehead> that since the "alter" command is rather slow, I could speed it up about 2 fold by changing one selection to match the other, rather than changing both into glycines. This newer version of "fitting.py" is now available at: http://adelie.biochem.queensu.ca/~rlc/work/pymol I've also added some documentation to it, so typing "help fitting" after having done "run fitting.py" will print the documentation out to your screen. So if you have downloaded "fitting.py" before 1pm EST today, you might want to try this new and improved version. :) The older version "fitting_v1.py" is also available (but also with documentation added) in case I've managed to introduce new bugs that I haven't already squashed. 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
