Hi Jan,
Did you use the TLS refinement for your data? I have had the similar
problem with the multi-group TLS refinement. After the first run the
resulting pdb file contained unreasonably small atomic B factors for
many atoms comparing to the Wilson plot B factor. They seemed to be the
TLS-B factors instead of the expected residual B factors. The TLSANL
could have not produced the total nor residual B factors when given
that file (plus the .tls file from that Refmac run). Moreover, I
couldn't use this file as an input for the next Refmac refinement as it
was not stable. Interestingly, I have had no problem when using one
group only in the TLS step. The version of Refmac was 5.2.0019. Do you
observe by chance a similar case?
Aleks
On 11 Nov 2008, at 01:36, Jan Abendroth wrote:
Hi all,
I have a number of low-ish resolution data sets that show a strange
B-factor behaviour:
All are just better than 3AA resolution, collected on a strong
synchrotron beamline. Some, yet not tremendous radiation decay.
Wilson scaling, obviously not very reliable at this resolution, gives
me a Wilson B of about 40, already a low number. Refinement in refmac5
(5.5.0053) with individual B-factors refinement leads to an average B
factor of around 16 with several individual B factors hitting the B=2
limit...
When I convert Is to Fs in truncate simply using the square root,
things get even a bit worse, the average B now is 14.
When I try to do an overall B-factor refinement, still individual
B-factors appear in the output file.
refinement details: 2.8AA resolution,medium ncs for two ncs related
chains, no riding hydrogens, simple scaling, MKLF target, isotropic B
factors
Rwork: 0.206, Rfree=0.286, bonds=0.018, angles=1.89 ... obviously I
could retrain a bit more...
Any ideas how to handle this? Basically, my question is: how do I get
the overall B factor to realistic numbers?
Thanks a lot for any hints
Jan
--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island, WA, USA
work: JAbendroth_at_decode.com
home: Jan.Abendroth_at_gmail.com
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