Hello Rakesh,
yes, you are right. In contrast to all modern refinement programs,
sfcheck neither applies TLS nor the superior mask bulk solvent
correction (it applies the Babinet bulk solvent correction by
double-exponential scaling). As a result, the R-factors from sfcheck are
higher than those from the refinement program.
Annoyingly, I have to discuss/explain this discrepancy in R-factors
every time when I want to deposit a refined X-ray structure with the
Protein Data Bank ...
Best regards,
Dirk.
Am 06.07.10 17:05, schrieb Rakesh Joshi:
Hello,
I refined my structures using REFMAC5 ( using TLS in combination ). When i used
the SF-Check
program, my R-values are ~5% higher than in those reported by refmac. Is this
due to the fact that SF-check does bulk solvent calculations differently and
does not account for TLS refinement?
Also, when i used TLSANL to put in my total B factor in the pdb file I only get
3 sets of numbers instead of( what i expected) 6 sets(ie. last three entries have
values="0").
For example:
ATOM 246 C6 DA C 13 -29.692 15.902 14.379 1.00 36.42 C
ANISOU 246 C6 DA C 13 3267 5459 5110 0 0 0 C
Cheers
Rakesh
Graduate student
Purdue University
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
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D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
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