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 _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
