[ccp4bb] TLSMD Alignments

2010-08-24 Thread Michael Thompson
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


Re: [ccp4bb] TLSMD Alignments

2010-08-24 Thread Roberto Steiner

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