[phenixbb] Refinement of B-factors at low resolution

VAN RAAIJ , MARK JOHAN mjvanraaij at cnb.csic.es
Sat Mar 23 11:10:51 PDT 2013


At 3.2 A resolution I don't think Phenix (or any other program, or  
anyone) can reliably determine a Wilson B beyond giving a rough idea  
of the range, because you have too few data points and the data points  
you have are "contaminated" by influences of the peaks and troughs due  
to regular repeats in secondary structure elements (and you don't know  
the amount of these secondary structure elements...), so I wouldn't  
worry about it.
Mark
PS Perhaps Phenix should not quote it with apparent four-digit  
precision, i.e. 66.45, at least at this resolution, in case people  
take this number too seriously?

Quoting Florian Brückner <florian.brueckner at psi.ch>:

> Thanks, Pavel.
>
> So you don't think that the difference between Wilson B (66.45  
> according to phenix) and average B (52 after refinement) is still  
> too large? Where did you take the statistics from? Is that published  
> anywhere?
>
> Best regards
>
> Florian
>
> Am 22.03.2013 um 07:09 schrieb Pavel Afonine <pafonine at lbl.gov>:
>
>> Hi Florian,
>>
>> I think it is pretty convincing that refinement went all right and  
>> the mean B you get is what it actually is. Also I just looked at  
>> the files that you sent me the other day and I did not notice  
>> anything suspicious.
>>
>> Pavel
>>
>> P.S.: Sorry if you received multiple copies of this email: I was  
>> trying to attach a tiny image with some PDB statistics but our  
>> server did not let me do it.
>>
>> On 3/21/13 1:00 AM, Florian Brückner wrote:
>>> Dear Pavel
>>>
>>> yes, the refinement did converge. I did 6 macrocycles and in  
>>> separate runs started from different average atomic B-factors of  
>>> 32, 66 and 97 keeping the distribution as in the original high  
>>> resolution molecular replacement model from the same crystal form  
>>> (i.e. adding 0, 34 and 65 to all atomic B-factors in the starting  
>>> pdb). In all cases after 6 macrocycles I get an almost identical  
>>> distribution of B-factors and also average B-factor of about 52.  
>>> Also setting all B-factors to the same value of 66 gave a similar  
>>> distribution after refinement with an average of 52. However, in  
>>> the latter case the R-free was about 2% higher compared to  
>>> starting from the original distribution, but it dropped by about  
>>> 1% during refinement.
>>>
>>> Best regards
>>>
>>> Florian
>>>
>>>
>>> Am 21.03.2013 um 06:40 schrieb Pavel Afonine <pafonine at lbl.gov>:
>>>
>>>> Hi Florian,
>>>>
>>>> I'm glad it works now. Regarding difference between Wilson B and  
>>>> mean refined B: well, it's hard to quantify what's "too low" or  
>>>> "too different". Average refined B may deviate from Wilson B and  
>>>> the difference in your case does not seem to be terribly large.
>>>> Did the refinement converge? What if you do say 10 or 20  
>>>> macro-cycles instead of default 3? Will B-factors further change  
>>>> between macro-cycles?
>>>>
>>>> Pavel
>>>>
>>>> On 3/19/13 7:37 AM, Florian Brückner wrote:
>>>>> 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
>>>>
>>>> _______________________________________________
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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
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>
> -------------------------------------------------------------
>
> 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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