Dear Micheal,

As you say, the effect is probably arising from the different packing environment of your NCS-related molecules. Once you've taken TLS groups into account NCS restraints might even perform better.

Cheers,
Roberto

On 24 Aug 2010, at 21:15, Michael Thompson wrote:

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

---
Dr. Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax   +44 (0)20-7848-6435
e-mail roberto.stei...@kcl.ac.uk

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