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


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