Thank you Jared for the detailed explanation! Neena
On Tue, 9 Apr 2019 at 12:35, Jared Sampson <jared.samp...@columbia.edu> wrote: > Hi Neena - > > PyMOL shows all the potential H-bonds, but not all of them will be formed > at all times. Any single proton can only participate in one H-bond at a > time, but remember a crystal structure is an average structure based on the > ensemble of states present in the protein crystal (or on the EM grid for > cryo-EM structures). It's ok to have "too many" polar contacts...it just > means the atoms have options for where to interact. > > Also, a carbonyl oxygen has 2 lone pairs, so can accept 2 H-bonds. See > perhaps McDonald & Thornton, JMB (1994) > https://doi.org/10.1006/jmbi.1994.1334 for a more detailed discussion. > > Hope that helps. > > Cheers, > Jared > > > On April 4, 2019 at 11:25:17 PM, Neena Susan Eappen ( > neenasusan...@gmail.com) wrote: > > Hello PyMOL users, > > Hydrogen bond finder on Pymol sometimes gave me unexpected observations > like: > more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on. > This is even after setting H-bond center cutoff to 3.0 A. Any insight would > be appreciated. > > Thank you for sharing your knowledge, > Neena > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > >
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