Hi, I am running version 1.7.2.1 from the svn (revision 4088) and the bug with dynamic_measures persists. Unsetting it as in that link corrects that issue though.
I can send you my files that find the error if you would like. Matt On 08/27/2014 11:19 AM, Thomas Holder wrote: > 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 ------------------------------------------------------------------------------ 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
