I agree that it would certainly be bad if your model was inconsistent
with the Wilson B. When I first ran into people who were worried about
this I recommended that they calculate the Wilson B of their model, not
look at the average B as a proxy. You can calculate structure factors
from your model and feed those into a Wilson B calculator and get the
proper value.

   When you do this you find pretty quickly that a refinement program
has to be screwed up pretty badly for it to create a model with even a
small difference between the observed and calculated Wilson B. If your
model is off only a little the R value shoots up! Other than when
debugging refinement code, I have never seen a refined model where there
was any significant difference between the calculated and observed
Wilson B. This problem simply doesn't come up.

   Try it for yourself and see.

   When you see a difference between the Wilson B and the average of the
B's in your model, all you are seeing is that you have a variety of B
factors and that is not a surprise. I would be worried if all my B
factors were equal!

   High B factors are not a problem to be fixed! Some atoms do move
more than others. Why would you expect otherwise?

Dale Tronrud

On 10/14/2016 12:28 AM, Carlos CONTRERAS MARTEL wrote:
> Sunanda,
>
> As "common people", ... "agreement" don't means for me "equals" ...
>
> So I hope I'm not so "incorrect" if I keep one mind the Wilson B as the
> model
>
> refinement goes and the average B factor changes with different strategies.
>
> If you are still worry about your Bfactor, you could try TLS, using the
> right approach could
>
> improve your results.
>
> All the best
>
> Carlos
>
>
>
> On 10/13/16 18:42, Dale Tronrud wrote:
>> It seems to be common for people to make the incorrect assumption
>> that the average of the atomic B factors in the PDB file should equal
>> the Wilson B. The Wilson B is actually a weighted average of the
>> individual B factors where the weighting is rather mysterious, but the
>> small B factors have much higher weight than the larger ones. While the
>> Wilson B is simply a property of your data set the average of the atomic
>> B factors will also depend on choices you have made in building your
>> model.
>>
>> In your case the core of your protein does have B factors that match
>> your Wilson B. The fact that you have loops that have larger B's
>> doesn't really mean there is a problem, because those atoms don't
>> contribute much to the higher resolution reflections and don't come into
>> the calculation of the Wilson B.
>>
>> The average of your B factors will increase if you choose to build
>> model for more disordered regions, while the Wilson B will, of course,
>> remain the same. The average B factor will be larger, for example, if
>> you are more aggressive in building water molecules. This does not
>> indicate a problem but is an unavoidable consequence of your choice to
>> take more risks.
>>
>> Dale
>>
>>
>>
>> On 10/13/2016 12:16 AM, sunanda williams wrote:
>>> Sorry for not making the problem clear!
>>> The overall B factor for the 3.0 A structure is around 98.00 A*2. Most
>>> of the deposited structures in the PDB site around this resolution
>>> has an av B around 70 A*2....
>>> All other statistics looks fine. I got a warning message while trying to
>>> upload the structure in PDB that 98 was higher than the norm!
>>> The reason why the structure has such a high B factor could be due to
>>> disordered loops... All the same I was wondering how acceptable this
>>> structure would be to picky reviewers..
>>> And 'better the B factors' means bring them down...sorry couldn't phrase
>>> it 'better'! I am going to try doing refinement with group B factors!
>>> Would that help?
>>> Thanks Robbie, I think this I need to make the best of the model I have.
>>> Prof. Sekar will try PDB_redo..Thanks!
>>>
>>>
>>>
>>> On Thu, Oct 13, 2016 at 11:41 AM, Pavel Afonine <[log in to unmask]
>>> <mailto:[log in to unmask]>> wrote:
>>>
>>> I fully agree with Dale in not understanding what the problem is.
>>> Perhaps I have a better chance if you clearly explain what exactly
>>> you mean by "is there any way to better the B factors".
>>> Pavel
>>>
>>>
>>> On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud
>>> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>>
>>> I'm sorry but I don't understand what your problem is. Do
>>> you think
>>> the B factors are too small for a 3A data set? A range of 70 to
>>> 75 is a
>>> little smaller than usual but probably not out of bounds.
>>>
>>> Dale Tronrud
>>>
>>> On 10/12/2016 7:59 PM, sunanda williams wrote:
>>> > Hi all,
>>> > I have a structure at 3.0 A and R/Rfree of 24/28. The mean B
>>> value is
>>> > around 98. The B value is especially high at the N terminus
>>> and two loop
>>> > regions (around 120-150 AA).
>>> > The rest of the structure averaged around 70-75. Has anyone
>>> faced such a
>>> > scenario? How reliable is the structure and is there any way
>>> to better
>>> > the B factors.
>>> > Any help is appreciated.
>>> > Thank you!!
>>>
>>>
>>>
>