Dale,
I have had a similar problem with two of my entries. However, if I take
the TLS information from the PDB header and put it in a "in_tls.tls" file
that I feed into REFMAC (0 cycles, just structure factor computation), I
can reproduce the R-factors within 0.1% or less.
It is just the order of the numbers that matters but this is described in
the REFMAC documentation.
Cheers,
Ulrich
On Wed, 12 Mar 2008 22:20:58 +0100, Dale Tronrud
<[EMAIL PROTECTED]> wrote:
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
--
Prof Ulrich Baumann
Departement für Chemie und Biochemie
Freiestrasse 3
Ch-3012 Bern, Switzerland
phone + 41 (0)31 631 4320/4343
fax + 41 (0) 31 631 4887
