This scaling is a real pain..
However If you look at the plot of <Fobs> v <Fcalc> ( a loograph under
Rfactor v resolution plots)
it often gives a clue. I think it is usually due to poor estimation of
the bulk solvent correction, espec if the model is incomplete. (We could
discuss that if there was any interest).
There are 2 main causes - incomplete model (eg no side chains) and
missing or poorly estimated low resolution <Fobs> which are the very
terms used by the bulk solvent estimation.
If it is due to incomplete model it will probably get better as the
model improves. If the low resolution strong data is lost you may do
better to only refine over a more limited range; eg RESLN 12 2.8
instead of the default RELN 100 2.8
Eleanor
junfeng liu wrote:
Hi Jan,
You can try :bulk scale ;set bulk solvent B value to 200.0 and lower
the weight to 0.5 or 0.3 . Sometimes it does work.
Good luck!
liu
Lijun Liu wrote:
If the cell dimensions are huge and this is what dictates the
resolution/diffractibility, I will think the results may be
reasonable, at least theoretically. In this regard, further stronger
X-ray helps better resolution. LJL
On Nov 10, 2008, at 5:36 PM, 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 <http://Jan.Abendroth_at_gmail.com>
Lijun Liu, PhD
Institute of Molecular Biology
HHMI & Department of Physics
University of Oregon
Eugene, OR 97403
541-346-5176
