Hello Joel, Actually I am using VINA that indeed provides us with these RMSD values. However the goal is to compare the docking poses with the X-ray structure containing another (but very similar in terms of the functional groups) ligand. I've already tried some pymol built-in commands like pair_fit but I could not adapt it to the multi-model pdb in order to select "on-the-fly" the pose which has better similarity to the pose observed in the X-ray structure. Cheers, Enrico
пт, 25 мар. 2022 г. в 01:28, Joel Tyndall <joel.tynd...@otago.ac.nz>: > > Hi Enrico, > > Which docking protocol are you using as this may already have RMSD to a > reference ligand and presentation of best poses (based on scoring) > > Joel > > -----Original Message----- > From: Enrico Martinez <jmsstarli...@gmail.com> > Sent: Friday, 25 March 2022 2:11 AM > To: pymol-users <pymol-users@lists.sourceforge.net> > Subject: [PyMOL] Analysis of docking results in multi-model format > > Dear Pymol Users! > I am dealing with the analysis of the results of protein-ligand docking poses > representing the multi-model pdb. I need to find a possibility (e.g. via > some script that could be executed in the pymol) to compare each docking pose > with the X-ray structure (loaded as the separate model in pymol) in order to > find automatically the model (= docking solution) which may fit better to it > (e.g. via estimating RMSD of some part of the ligand in each docking solution > compared to the X-ray structure). > > Assuming that the both pdbs ((docking poses, and X-ray structure)) have been > superimposed (based on the protein atoms) how could I automatically switch to > the model (in the ensemble) with the identical position of the ligand as in > the X-ray structure? I would be grateful for any suggestions With kind > regards, Enrico > > > _______________________________________________ > PyMOL-users mailing list > Archives: > https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7C5801f6d4300c4429df4008da0d996aa8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637837249971556989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2FH4rWyrcccM8UDMCjpXhzfhvbWIRK7iVxT3WTHhd11Q%3D&reserved=0 > Unsubscribe: > https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7C5801f6d4300c4429df4008da0d996aa8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637837249971556989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=W1bYxrtg1zExUmoFtA3srAUsOc8PAODG2QimqwEY%2FQw%3D&reserved=0 _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
