just as an update of my first topic. Is there any possibility to associate any plugin or external tool (rdkit) to calculate pharmacophore model for each docking pose loaded in multi-model format (i) as well as for the ligand in X-ray structure (ii) and then compare i with ii in order to find instantly the docking pose which is more similar to X-ray structure according to some part of the pharmacophore shared between the both molecules ?
чт, 24 мар. 2022 г. в 14:11, Enrico Martinez <jmsstarli...@gmail.com>: > > 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: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
