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Hi Thomas Perhaps this is a Pymol version issue? I just tried this (with the second command of yours) with the original coords and get the same as Baptiste. I tried this on v. 1.8.2 open source Pymol in Win10 laptop. With the fixed coords I just sent back, the result is the correct 0.032 A. cheers, Marko On 26/07/2018 09:26, Thomas Holder
wrote:
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, ThomasOn 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 -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@cam.ac.uk +44 (0)1223 766 044 @HyvonenGroup http://hyvonen.bioc.cam.ac.uk |
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