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 -- ------------------------------------------------------------------------------ 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
