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
>>
>>
>>
>
>
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