Check out Robert Campbell's Pymol script repository. I think align_all_to_all.py should do what you want, including exporting RMSD values.
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Jed On 1/7/2014 11:58 AM, Om Shiv wrote: > Hello All > > I am a new user to Pymol and Python. > > I have a PDB Structure with single chain (A) and I have modeled 500 > single point mutants of this wild structure. > > Now for each such 500 modeled structures, I would like to calculate RMSD > (ALL ATOMS) with the wild type PDB structure. > > Can anybody help me with the script to automate calculation of 500 RMSD > calculations using PYMOL ? > > Secondly, what threshold value of RMSD can be considered above which we > can say that the mutant structure is considerably different than the > wild type ? > > Thanks in advance. > > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > > > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- ------------------------ Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
