Not knowing what your molecule looks like, could it be automorphism?
> -----Original Message----- > From: Baptiste Legrand <bap.legr...@gmail.com> > Sent: Wednesday, July 25, 2018 9:17 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and > from a docking > > Dear all, > > I tried to calculate a rmsd value between ligands from a crystal structure and > after docking. The two molecules share similar nomenclatures and are really > well superimposed. I think that the RMSD should be < 1 A. I used the following > lines: > > alter all,segi="" > alter all,chain ="" > rms /ligand_crystal////*, /ligand_docking////* > > It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the > pair_fit function, pymol completely return one molecule and also write > "ExecutiveRMS: RMS = 6.146 (51 to 51 atoms)". I should have missed > something... > > thanks for the help, > All the Best. > > Baptiste > > > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------------------------------ 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
