Hi Nathan, Thank you very much for the files and instructions. I can reproduce the problem. I haven't seen this before and don't know yet what's going wrong, we will investigate.
Cheers, Thomas > On Jun 28, 2018, at 10:50 AM, nclem...@cs.utexas.edu wrote: > > The alignment in this example is nearly perfect. Even the residues left > out of the fitting have perfect matches at the sequence level (as can be > seen by saving the super object and turning on the sequence alignment and > contact_all). > > PyMOL>load 1AY7_u.pdb, test > CmdLoad: "1AY7_u.pdb" loaded as "test". > PyMOL>load 1AY7_b.pdb, gold > CmdLoad: "1AY7_b.pdb" loaded as "gold". > PyMOL>select contact_rec, gold & chain R & (all within 10 of gold & chain > L) & n. ca > Selector: selection "contact_rec" defined with 33 atoms. > PyMOL>select contact_lig, gold & chain L & (all within 10 of gold & chain > R) & n. ca > Selector: selection "contact_lig" defined with 33 atoms. > PyMOL>select contact_all, contact_rec + contact_lig > Selector: selection "contact_all" defined with 66 atoms. > PyMOL>super gold & contact_all, test, cycles=0 > MatchAlign: aligning residues (66 vs 185)... > MatchAlign: score 143.882 > ExecutiveAlign: 58 atoms aligned. > Executive: RMS = 0.524 (58 to 58 atoms) > > <1AY7_u.pdb><1AY7_b.pdb> -- 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
