Hi Matt, I just double-checked, this was a major refactoring of the dynamic_measures setting which didn't make it into Open-Source PyMOL yet. So if you don't have access to Incentive PyMOL, then please use the workarounds.
Cheers, Thomas On 27 Aug 2014, at 11:25, Matthew Baumgartner <mp...@pitt.edu> wrote: > 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 -- 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
