Hi Mohammad, If there is already a ligand in the pocket and you just want to know its center x,y,z, you can simply type:
centerofmass organic Or if there are multiple organic molecules and you are interested in one with the unique residue name "LIG": centerofmass resn LIG I wound't call that "finding" a pocket though. Cheers, Thomas > On Jul 11, 2017, at 7:42 PM, Mohammad Goodarzi <mohammad.goda...@gmail.com> > wrote: > > Hello, > > I am wondering whether it is possible to find the pocket of a protein in > Pymol? > lets say I have a protein and a ligand inside the pocket. I want to estimate > the x, y and z > > Best Regards, > Mohammad -- 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
