Hi Guillermo, Thanks very much for your suggestions. I will try this torsion angle potential term and the TALOS-N.
Best Si On Wed, Apr 9, 2014 at 5:54 PM, Bermejo, Guillermo (NIH/CIT) [E] < guillermo.berm...@nih.gov> wrote: > Hi Si, > > Something that may help is using a statistical torsion angle potential > term. Although no substitute for experimental restraints, it will at least > help getting rid of rotamer outliers, so that you are left with plausible > ones. (Note that, in the standard approach, this term applies to all the > residues. It also affects the backbone, improving the Ramachandran > statistics.) > > You can access the latest version of this potential, called "torsionDBPot" > [Bermejo et. al. (2012) Protein Sci. 21: 1824], through the Python > interface. For an example on how to set it up you can take a look at > xplor/eginput/gb1_rdc/refine.py, where "xplor" refers to your Xplor-NIH > directory. > > Additionally, you may want to explore TALOS-N, which now predicts chi1 > torsion angles. > > I hope it helps. > > Best, > > Guillermo > > ________________________________________ > From: Si Yan [s...@udel.edu] > Sent: Wednesday, April 09, 2014 5:06 PM > To: xplor-...@nmr.cit.nih.gov > Subject: [Xplor-nih] A question about rotamers > > Hello Charles and others, > > I have refined some structures from solid-state NMR restraints. When > we compare the NMR structure of our protein with X-ray structures with > different binding partners, we find some PHE's aromatic rings present > rotamer difference between NMR structure and the X-ray structures. It is > hard for us to judge that this rotamer difference is a result of real > difference in structures or it is just because of lacking of restraints to > constrain the side-chain torsion angles. > We only used distance restraints and backbone torsion angle restraints > for the structure refinements. In our NMR restraints list for the > structure refinement, there is no restraints from the atoms of the aromatic > rings. > My question is there any way to constrain the side-chain torsion angle > in Xplor-NIH? > I saw a function named correctSymmetricSidechains in selectTools module. > > But I am not sure if this the correct thing I should include in my > refinements. If this is what I could use, how can I use it properly? > > > Thanks very much! > > Best > Si > > > -- > Si Yan > Department of Chemistry and Biochemistry > University of Delaware > Newark, DE, 19716 > Email to s...@udel.edu<mailto:s...@udel.edu> > Phone: 302-831-8624 > -- Si Yan Department of Chemistry and Biochemistry University of Delaware Newark, DE, 19716 Email to s...@udel.edu Phone: 302-831-8624
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