Hi Dale,
to my knowledge, sfcheck calculates the contribution of the bulk
solvent using the double-exponential scaling model (Babinet model),
but not using the mask model that REFMAC applies per default. I
sometimes have to discuss similar R-factor differences with RCSB upon
PDB submission of refined models ...
Best regards,
Dirk.
Am 12.03.2008 um 22:20 schrieb Dale Tronrud:
Hi,
I am looking over a number of models from the PDB but have been
unable to reproduce the R-factors for any model that was refined
with Refmac and contains TLS parameters. I usually can't get within
5% of the reported value. On the other hand, I usually do pretty
well for models w/o TLS.
An example is the model 1nkz. The PDB header gives an R value
of 17% but even when I use tlsanal in CCP4i to generate a PDB with
anisotropic B's that mimic the TLS parameters I get an R value of
22.4% using SFCheck. (I'm not implying that I suspect any problem
with 1nkz, in fact I have every reason to believe this is the great
model its published stats indicate.)
I've found a CCP4 BB letter that stated that SFCheck does not
pay attention to anisotropic B's but that letter was dated 2002.
I hope this limitation has been removed, or at least the output
would mention this limitation.
Setting up a refinement in Refmac involves a large overhead,
since even for zero cycles of refinement the program insists on
a complete stereochemical definition for the strange and wondrous
groups in this model. I would just like to verify the R factor
and calculate a proper map for inspection in Coot. Since I have
many models I would like to look at, I would like a simple procedure.
I did set up a Refmac run for another model, for which I do
have all the .cif's required, but even after refinement I was not
close to the reported R.
I see that the models I'm interested in are not present in the
Electron Density Server, so I suspect I'm not alone in fighting
this battle.
Any advice would be appreciated,
Dale Tronrud
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Dirk Kostrewa
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Ludwig-Maximilians-University
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Germany
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