Hmm, this should've been replied to the list. The info may be useful to others.
Tsjerk ---------- Forwarded message ---------- From: Tsjerk Wassenaar <tsje...@gmail.com> Date: Mon, Nov 9, 2009 at 5:02 PM Subject: Re: [PyMOL] asymmetric transformation matrices To: Thomas Evangelidis <te8...@mbg.duth.gr> Hi Thomas, You're not doing what you think you're doing. > # a function to measure Ca distances of oposite pairs of superimpossed > chains (the proteins must have the same aa composition) > def check_for_symmetry(tstruct, qstruct): > # align the pair > cmd.fetch(tstruct) You fetch the first structure, which is placed in state 1 > cmd.extract(pdb2entry[tstruct]+"1", tstruct + " and chain "+ > pdb2entry[tstruct][-1:] + " and not hetatm") You extract part of that structure, which is removed from the state > cmd.fetch(qstruct) You fetch the other structure, which is also loaded into state 1 > cmd.extract(pdb2entry[qstruct]+"1", qstruct +" and chain "+ > pdb2entry[qstruct][-1:] + " and not hetatm") You extract part of that structure > print "Aligning "+pdb2entry[tstruct]+"1"+" with "+pdb2entry[qstruct]+"1" > cmd.align(pdb2entry[tstruct]+"1", pdb2entry[qstruct]+"1") > #cmd.do("cealign "+pdb2entry[qstruct]+"1, "+pdb2entry[tstruct]+"1") > # align the symmetric pair > cmd.fetch(tstruct) You fetch the first structure again, but this time it's appended to state 2 > cmd.extract(pdb2entry[tstruct]+"2", tstruct + " and chain "+ > pdb2entry[tstruct][-1:] + " and not hetatm") You try to extract chain A again. But that is tried on state 1, while that state has no chain A anymore. The object is empty! > cmd.fetch(qstruct) Same story for the other object > cmd.extract(pdb2entry[qstruct]+"2", qstruct +" and chain "+ > pdb2entry[qstruct][-1:] + " and not hetatm") Empty object... Then in the next part you calculate the RMSD of distances in an empty object (all 0) and the aligned one. That RMSD ends up close to the actual RMSD from the alignment (restricted on CA atoms: 0.280), for obvious reasons. I hope this helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ 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