Hi Nathan, Sounds like you are doing everything correct. Would it be possible to send me the input files?
Thanks, Thomas > On Jun 26, 2018, at 10:58 AM, Nathan Clement <nathanlclem...@gmail.com> wrote: > > Hi, > > I'm trying to compute the interface RMSD (iRMSD) between two protein pairs > that are highly similar (might have a few missing residues, but are otherwise > identical). Right now, my code does something like the following for protein > pairs "gold" and "test" (receptor has chains A+B and ligand has chains C): > > PyMOL>select contact_rec, (gold & chain A+B) & all within 10 of (gold & chain > C) & n. ca > PyMOL>select contact_lig, (gold & chain C) & all within 10 of (gold & chain > A+B) & n. ca > PyMOL>align gold & contact_rec + contact_lig, test, cycles=0 > Match: read scoring matrix. > Match: assigning 82 x 445 pairwise scores. > MatchAlign: aligning residues (82 vs 445)... > MatchAlign: score 257.500 > ExecutiveAlign: 67 atoms aligned. > Executive: RMS = 14.161 (67 to 67 atoms) > > This seems to suggest that, even with cycles=0, 82-67=15 atoms were not > included in the alignment. When I look at the alignment (object=aln), it > appears that most of the "missing" residues from this alignment have the same > residue name, are matches in the sequence alignment, and are in a nearby > location. > > Is it possible to force align to give the full RMSD calculation? super has > the same issue, and I'm concerned that using something like rms or fit won't > work because the "gold" and "test" have different residue numbering (and > might be missing residues so it's not always possible to give them an > equivalent numbering). > > Does anybody have any suggestions? > > Thanks in advance, > > Nathan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ 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
