Hello Santhosh-- > > I want to refine a protein against RDC's and have been following the scripts > in > gb3_rdc and other examples. The protocol I followed is very similar to the > protocol given in the scripts but just to check a few things, I have not done > any > minimization in the catesian space but only in the torsional space. I observe > that there are peptide bond planarity violations (omega torsional angle) in > that. > > That is odd as I thought IVM only uses phi and psi only as coordinates. The > starting structure does not have any omega angle discrepancies. But the > refined > structures have it. Can you please let me know where should I be looking for > the > possible cause of error?
By default, all torsion angles are allowed to move. In more modern scripts, you can make omega rigid by passing the fixedOmega=True argument to protocol.torsionTopology. In the old scripts in gb3_rdc, you should call the function selectTools.IVM_groupRigidBackbone(dyn) before the call to dyn.autoTorsion() Now, normally, you should not have significant omega violations- that points to something else amiss. Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
