Hi Charles, Thanks! This information is very helpful. I have tried the torsionDB term, and the RAMA energy does decrease a little. I will include the torsion angles from TALOS-N for the refinement.
Best Si On Thu, Apr 10, 2014 at 10:15 AM, Charles Schwieters <char...@schwieters.org > wrote: > > Hello Si-- > > > > > 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? > > Guillermo's suggestions of trying torsionDB and TalosN may well help > you immensely. > > To complete the conversation, however, I wanted to follow up with a > bit about symmetric sidechains. The presence of symmetric sidechains > (PHE, TYR, ASP, ARG, and GLU) can degrade the apparent overall heavy > atom precision if atoms which are chemically equivalent, but named > differently are in close proximity. The chi2, chi3 or chi5 torsion > angles which define the symmetry operations are given reduced ranges > to remove the degeneracy. correctSymmetricSidechains will make the > appropriate changes such that the torsion angles are in the correct > ranges, and it is automatically called when you load a structure using > protocol.loadPDB or protocol.initCoords. Additionally, > protocol.initDihedrals by default adds additional restraints such that > the symmetry-reduced angle ranges are maintained throughout a > calculation. > > So while torsionDB will add knowledge-based information,and TalosN can > give you experimentally based restraints, one should be aware of the > symmetry issue so that conformations which are very close don't appear > to have chi angles which differ by 180 degrees. > > best regards-- > Charles > -- 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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