George & other TLS experts,
Does this explain why TLS refinement sometimes gives great R-factor statistics, but individual B's that are very low, much lower than the Wilson B? (And, I guess, the trace of the U matrix high is "inflated".). I ran across this behaviour some months ago with two structures at ~1.3 & 1.4 A. TLS really helped, but the B's, at first glance, seemed absurd. The TLSANL-converted B's were OK (in line with Wilson B).
From a practical point of view (in Refmac), to have the B's drive to smaller values, while the U-trace goes up, is no problem...until the B's need to go negative (or are artificially halted at, e.g., B = 2.0). Problem, or not?
Dave
~~~~~~~~~~~~~~~~~~~~~~~~
David W. Borhani, Ph.D.
Structural Biology Group Leader
Chemistry Department
Abbott Bioresearch Center
Vox: 508-688-3944
Fax: 508-754-7784
Email: [EMAIL PROTECTED]
Smail: Abbott Bioresearch Center, Inc.
100 Research Drive
Worcester, MA 01605 U.S.A.
http://abbott.com/abbottbioresearch/
~~~~~~~~~~~~~~~~~~~~~~~~
| "George M. Sheldrick"
<[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED] 05/19/2006 01:27 PM |
|
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There is another good reason why you should run TLSANL to produce the
PDB file for deposition after doing a TLS refinement in REFMAC: the
ANISOU cards it produces should in principle be unique for a given
structure, but the TLS matrices and additive isotropic B's are not! You
can add a constant value to these B values for all atoms in the same TLS
group and subtract it from the diagonal elements of the T tensor for
that group, and the fit is unchanged. In other words REFMAC refines one
parameter too many per TLS group, and if it were able to do a full
matrix refinement this would cause it to blow up with a singular matrix
(Garib: please do not interpret this as a criticism, the REFMAC approach
is a good practical solution to a tricky problem and we make good use of
the TLS refinement in REFMAC).
Possibly some future version of a refinement program will apply TLS
restraints rather than constraints, this could be programmed in a way
that would refine the Uij values directly and so avoid this problem. The
deposition of restrained Uij values would then be on a par with the
deposition of restrained atom coordinates (which we do all the time).
George
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
