Hi Baptiste, These files look good to me, I get:
PyMOL>rms Crystal_Rfp, Vina_Rfp Executive: RMSD = 0.032 (51 to 51 atoms) Is it possible that you tried with a multi-model (multiple poses) pdbqt file before? If that's the case, specify "mobile_state" and/or "target_state": PyMOL>rms Crystal_Rfp, Vina_Rfp, mobile_state=1, target_state=1 Executive: RMSD = 0.032 (51 to 51 atoms) See also "Notes" section here: https://pymolwiki.org/index.php/Align#Notes Cheers, Thomas > On Jul 26, 2018, at 9:42 AM, Baptiste Legrand <bap.legr...@gmail.com> wrote: > > Thanks for your answers. The molecule is the rifampicin. Please find attached > the pdb from the crystal structure and the pdbqt from autodock vina. May be > the format of one or both files is not correct. > > Best, > > Baptiste > > > Le 25/07/2018 à 18:57, Markus Heller a écrit : >> 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 -- 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
