On Tuesday, November 23, 2010, Paula Salgado wrote:
> Resolution is 1.5A, Wilson B is 11.8.
Right. So there you have it. The Wilson B is telling you straight from
the data that the expected B factors are on the order of 11.8
You reported your model as
> > > Average B value for main ch
Resolution is 1.5A, Wilson B is 11.8.
Does that mean that might values are more than within expected ranges? I
knew at this resolution B factors are considerably lower, but I was
suspicious that some seemed, so low, specially after recent problems of over
refinement of B factors with another prote
ne
Sent: Tuesday, November 23, 2010 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Low B-factors
Dear Paula,
I do not know about phenix, but the refmac5 output PDB file does not contain the
contribution from the TLS refinement (not sure I get the terminology right). In
order to get a
Dear Paula,
I do not know about phenix, but the refmac5 output PDB file does not contain the
contribution from the TLS refinement (not sure I get the terminology right). In
order to get an idea of the average B-values, you should run tlsanl on the
output of refmac5 with the keyword 'bresid true'.
On Tuesday, November 23, 2010, Paula Salgado wrote:
> Dear all
>
> I'm refining a 33kDa protein model and I have noticed that although all
> other statistics seem fine, B factor values are quite low,
What is the resolution?
What is the Wilson B?
> with many around
> 7-10A2 and average overall
Dear all
I'm refining a 33kDa protein model and I have noticed that although all
other statistics seem fine, B factor values are quite low, with many around
7-10A2 and average overall values as follows.
Total number of atoms in chain A 2378
Average B value for main chain
This scaling is a real pain..
However If you look at the plot of v ( 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 inter
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
TL
It might be possible that there's a problem in the low resolution
portion of your data. You could check the wilson plot to make sure it
looks normal at that range, and possibly change the low-resolution
cutoff refmac is using.
Pete
Jan Abendroth wrote:
> Hi all,
> I have a number of low-ish reso
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,
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 h
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
W
Are you using TLS? If so the B factors in the PDB file are relative to
the TLS parameters..
Or have you lost low resolution data - you can see that in many plots -
one in REFMAC gives v as a function of resolution?
If so you probably need to use SCALE SIMPLE - in gfact that is usually
the
First, Thank you all for the help and suggestions, it
truly resolved the issue.
First I reset the B factors to something close to the
Wilson B average (53). Then making sure the
B-solvent contribution flag was set and refining
isotropic b-factor I reran the job. The B-factors now
are reasonable
I am working with a small protein in a relatively high
space group p6322 and have good data to a modest 2.5 A
resolution. During the first rounds of restrained
refinement however the B factors drop to an average of
15 and as low as 2 A^3. This has the effect of
producing large amounts of negative
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