[phenixbb] Refinement of B-factors at low resolution
Florian Brückner
florian.brueckner at psi.ch
Tue Mar 19 07:37:17 PDT 2013
Dear Keitaro and Pavel,
thank you for your suggestions. I have now used the latest nightly build (1326). With this version, the average B-factor converges at about 52 A**2 and also the distribution is very similar, regardless with what B-factors I start the refinement (I tried average B-factors between 32 and 97). So clearly the behavior of this newest version is different from the version I have been using before (1.8.1 stable release 1168) and also from the latest stable release (1.8.2 stable release 1309), which behaves the same as 1168. To me the B-factors still look a bit too low, since the Wilson B-factor calculated by phenix is 66.45, the Wilson B-factor I determined manually from the linear part of the Wilson plot is 97.
Best regards
Florian
Am 19.03.2013 um 00:06 schrieb Keitaro Yamashita <yamashita at castor.sci.hokudai.ac.jp>:
> Dear Florian,
>
> Maybe you are using phenix-dev-1311 or earlier?
> I am afraid that you have experienced the bug that overall B-factor is
> not applied to individual atomic B-factors in certain cases, which I
> have also experienced recently. That bug was fixed in dev-1312 if I
> recall correctly.
>
> Hope it helps,
> Keitaro
>
> 2013/3/19 Florian Brückner <florian.brueckner at psi.ch>:
>> Dear all
>>
>> I am refining a structure at 3.2 A with phenix.refine using automatic
>> optimization of target weights, solved by molecular replacement with a 2.1A
>> structure of the same crystal form. Rwork=26%, Rfree=28%. I use individual
>> atomic B-factor refinement. The obtained distribution of B-factors after
>> refinement looks reasonable and quite similar to the distribution in the
>> higher resolution model, which I suppose would be expected, since it is the
>> same crystal form. However, the average B-factor does not change
>> substantially, i.e. if I start with the B-factors from the high resolution
>> model (average B-factor around 32 A**2) after 6 macrocycles the average
>> B-factor is still around 32 A**2. If I set all B-factors to the Wilson
>> B-factor determined by phenix.refine (66 A**2), after 6 macrocycles the
>> distribution of B-factors looks again very similar to the high resolution MR
>> model, but the average B-factor is still around 65 A**2. What should I make
>> of this? Is this an expected behavior at this resolution, i.e. the fact that
>> the absolute values of B-factors cannot be determined during refinement,
>> although a reasonable distribution can be obtained as judged by plotting
>> average B-factors vs. residue#? Since the average B-factor does not change
>> much during refinement, which average B-factor should I start refinement
>> with to end up with reasonable absolute values? I have manually determined
>> the Wilson B-factor from the linear part of the Wilson plot (4.5-3.2 A) to
>> be 97 A**2. This seems high to me. Would that be expected for the given
>> resolution, given that the 2.1A structure of the same crystal form has 32
>> A**2? I should add, that there is not a substantial effect of the average
>> refined B-factor on Rfree.
>>
>> Thanks for any comments or suggestions.
>>
>> Best regards
>>
>> Florian
>>
>>
>> -------------------------------------------------------------
>>
>> Dr. Florian Brückner
>> Laboratory of Biomolecular Research (LBR)
>> OFLG/102
>> Paul Scherrer Institut
>> CH-5232 Villigen PSI
>> Switzerland
>>
>> Tel.: +41-(0)56-310-2332
>> Email: florian.brueckner at psi.ch
>>
>>
>>
>>
>>
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-------------------------------------------------------------
Dr. Florian Brückner
Laboratory of Biomolecular Research (LBR)
OFLG/102
Paul Scherrer Institut
CH-5232 Villigen PSI
Switzerland
Tel.: +41-(0)56-310-2332
Email: florian.brueckner at psi.ch
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