Hi Engin,
you are correct, you have to run TLSANL and report the corrected B-
factor in your table 1.
Jürgen
On 4 Oct 2008, at 18:32, Engin Ozkan wrote:
Hi everyone,
I was in the middle of creating a "Table 1" for a finished structure
and was puzzled by one number. It is the average B factor,
especially in the case of TLS-refined structures. In this case, the
average reported by refmac in the header is the average of the B
factors in the pdb file, which I assume is the residual B factors
(right?) (A quick Baverage confirmed the number is the average of
numbers in the B column). If the reported average is really for
residual B factors, isn't this a bit misleading? In this case, the
average B was 17, but after I created total B factors with TLSANL,
average B was 25 A^2.
I think total B factors should be the one reported, but I am afraid
that might not have been the practice by many. It is such a petty
point, but with TLS becoming common, shouldn't users be warned more
about such issues? Or could Refmac report the average for total B
factors?
Engin
P.S. I hate to bring up the controversy about the reporting of TLS-
refined B factors (residual vs. full anisotropic, or refmac vs
PHENIX), but it may come to that.
-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
