Forget my last reply ;-) Marko is right, I didn't notice first because this is fixed in PyMOL 2.1. Some PDBQT atom types were not imported correctly in previous versions.
Cheers, Thomas > On Jul 26, 2018, at 10:21 AM, Marko Hyvonen <mh...@cam.ac.uk> wrote: > > Hi Baptiste, > > removing the data at the end of the HETATM lines from ca. character 70 > onwards fixed it. Not sure what these are. According to PDB 3.30 format, > 67-76 should be empty. Some of the elements were non-standard also (NA for N, > OA for O), but looks to be the numbers in the "empty" columns that bother > PyMOL (perhaps it should just ignore these?). > > A lot of other things I do not recognise in PDB files in you docked > rifampicin too, but those seem not to bother the analysis. > > See attached. RMSD 0.032 for 51 atoms. Not a bad docking pose! > > cheers, Marko > > On 26/07/2018 08:42, Baptiste Legrand 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 > > -- > > Marko Hyvonen > Department of Biochemistry, University of Cambridge > > mh...@cam.ac.uk > > +44 (0)1223 766 044 > @HyvonenGroup > > http://hyvonen.bioc.cam.ac.uk > > <Vina_Rfp3.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
