TLS in phenix does seem to lead to high B factors in some of our cases.
To check whether it was particular to our datasets , we rerefined some
similar structures to ours from the PDB and found that their B factors
increased to high values similar to our structure when run through the
same phenix.refine protocol.
Structure 1 Chain A original Average B 40.85 After Phenix with TLS
113.33 Chain B Original 50.1 After phenix TLS 121.11
Structure 2 Chain A original Average B 64.46 After Phenix with TLS
100.63 Chain B original 64.99 After Phenix TLS 103.5
Structure 3 Chain A original 46.44 After TLS 52.63 - so it does not
always happen
This of course only proved that our data was probably not exceptional it
was the protocol. It does not explain what is going on.
http://www.phenix-online.org/pipermail/phenixbb/2010-January/014374.html
seems to offer some explanation of the TLS scaling in phenix.
It may be the anisotropic component reduces the size of the actual B
factor back to closer to the values before TLS?
Best wishes
Nick
--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck, University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX
email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852 (Room G54a Office)
020-7631-6800 (Department Office)
Fax 020-7631-6803
If you want to access me in person you have to come to the crystallography
entrance
and ring me or the department office from the internal phone by the door
