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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