Hi Matt, this was a bug with the dynamic_measures setting. It was fixed in PyMOL 1.7.0. So please upgrade PyMOL or read this old post for workarounds:
http://sourceforge.net/p/pymol/mailman/pymol-users/thread/501949e8.2080...@users.sourceforge.net/ Cheers, Thomas On 27 Aug 2014, at 10:30, Matthew Baumgartner <mp...@pitt.edu> wrote: > Hi, > I ran into a bug with the find polar contacts function (distance with > mode=2) today. The problem arises when I was trying to find the hydrogen > bonds between a ligand and a receptor that had been processed with > reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A > bug/feature of reduce is that when it adds hydrogens, it gives all of > the newly added hydrogens a 0 as the atom index in the pdb file. > So what happens is when you try to find the polar contacts between the > ligand and the receptor, it draws a bond between a ligand atom and the > last hydrogen (which happens to be non-polar) which is 12 A away. I'm > guessing it is because pymol is using the atom index from the pdb. > One possible alternative would be to index based on the set of the atom > id, atom name, residue name, chain id, and residue ID, but I don't know > how feasible that is. > > The work around that I have found is to pass the receptor through babel > after processing with reduce. babel prot.pdb prot2.pdb , which > re-indexes the atom ids. > > Matt Baumgartner -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ 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
