[phenixbb] Refinement of B-factors at low resolution
Pavel Afonine
pafonine at lbl.gov
Sat Mar 23 09:10:47 PDT 2013
Hi Florian,
Wilson B is just an estimate, and your refined B reflect your data..
Assumptions made to derive Wilson B include uniformly distributed atoms
in the unit cell, same atom type and B-factor (what else?). This is not
quite true for protein crystals, which typically consist of atoms of
different kind, have different degree of disorder (B-factors), and they
kind of form some structure (definitely not randomly distributed in the
unit cell). So to me it's a miracle that oftentimes Wilson B closely
matches refined average B. We should acknowledge that when it doesn't
that's a valid possibility.
Regarding papers.. Exactly that plot I sent you before was not published
(I guess it did not go to the phenixbb for the reason Nat explained
yesterday), but the tools and methods are described here:
Afonine, P.V., Grosse-Kunstleve, R.W., Chen, V.B.,Headd, J.J., Moriarty,
N.W., Richardson, J.S., Richardson, D.C.,Urzhumtsev, A.,Zwart, P.H. &
Adams, P.D. (2010).*phenix.model**_vs_data**: a high-level tool for the
calculation of crystallographic model and data statistics*. J.
Appl.Crystallogr. 43, 669-676.
Urzhumtsev, A., Afonine, P.V. & Adams P.D. (2009).*On the use of
logarithmic scales for analysis of diffraction data*.ActaCryst. D65,
1283-1291.
Urzhumtseva, L., Afonine, P.V., Adams, P.D. &Urzhumtsev, A.
(2009).*Crystallographic model quality at a glance*.ActaCryst. D65, 297-300.
and the source of information used for all the analysis described in
above papers is PDB. Also, I guess, you can obtain that plot from PHENIX
GUI.
Pavel
On 3/23/13 6:53 AM, Florian Brückner wrote:
> 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
> <mailto: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
>>> <mailto: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
>>>>> <mailto: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
>>>>>> <mailto: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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130323/17e46b7e/attachment.htm>
More information about the phenixbb
mailing list