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