Hi All, I have a question for those of you familiar with the TLSMD webserver. I am working on a structure with slightly imperfect 3-fold rotational NCS. My most recent .pdb file has been generated using Refmac (followed by a little tinkering in Coot), and during refinement I have been imposing medium main chain and loose side chain NCS restraints, and my R-factors don't really improve if I loosen the restraints further. This is the .pdb file I've also used an input to TLSMD.
The results of TLSMD do show that the residuals appear to slowly plateau when breaking the chains into 19 or 20 groups (all three A,B,C seem to converge similarly). When I look at the alignments, the TLS groups created for each chain do not align with each other well. The alignment of groups gets slightly better as more groups are added, which is partially just an issue of the groups being smaller and looking closer I think, but there is still significant stagger between neighboring groups. Is this typical for a structure with NCS-related chains? It seems somewhat counterintuitive to my understanding of how symmetric proteins should work (if the TLS motions reflect actual motions of the molecule). Perhaps the difference in TLS grouping between chains results from differences in Biso for NCS-related atoms that result from crystal packing? Maybe someone can shed some light on the situation? Thanks a lot, Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu