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CCP4BB  December 2012

CCP4BB December 2012

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Subject:

Re: refining against weak data and Table I stats

From:

Douglas Theobald <[log in to unmask]>

Reply-To:

Douglas Theobald <[log in to unmask]>

Date:

Thu, 13 Dec 2012 10:07:56 -0500

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text/plain (139 lines)

On Dec 13, 2012, at 1:52 AM, James Holton <[log in to unmask]> wrote:

[snip]

> So, what I would advise is to refine your model with data out to the resolution limit defined by CC*, but declare the "resolution of the structure" to be where the merged I/sigma(I) falls to 2. You might even want to calculate your Rmerge, Rcryst, Rfree and all the other R values to this resolution as well, since including a lot of zeroes does nothing but artificially drive up estimates of relative error.  

So James --- it appears that you basically agree with my proposal?  I.e., 

(1) include all of the data in refinement (at least up to where CC1/2 or CC* is still "significant")

(2) keep the definition of resolution to what is more-or-less the defacto standard (res bin where I/sigI=2), 

(3) report Table I where everything is calculated up to this resolution (where I/sigI=2), and 

(4) maybe include in Supp Mat an additional table that reports statistics for all the data (I'm leaning towards a table with stats for each res bin)

As you argued, and as I argued, this seems to be a good compromise, one that modifies current practice to include weak data, but nevertheless does not change the def of resolution or the Table I stats, so that we can still compare with legacy structures/stats.


> Perhaps we should even take a lesson from our "small molecule" friends and start reporting "R1", where the R factor is computed only for hkls where I/sigma(I) is above 3?
> 
> -James Holton
> MAD Scientist
> 
> On 12/8/2012 4:04 AM, Miller, Mitchell D. wrote:
>> I too like the idea of reporting the table 1 stats vs resolution
>> rather than just the overall values and highest resolution shell.
>> 
>> I also wanted to point out an earlier thread from April about the
>> limitations of the PDB's defining the resolution as being that of
>> the highest resolution reflection (even if data is incomplete or weak).
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1204&L=ccp4bb&D=0&1=ccp4bb&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=376289
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1204&L=ccp4bb&D=0&1=ccp4bb&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=377673
>> 
>> What we have done in the past for cases of low completeness
>> in the outer shell is to define the nominal resolution ala Bart
>> Hazes' method of same number of reflections as a complete data set and
>> use this in the PDB title and describe it in the remark 3 other
>> refinement remarks.
>>   There is also the possibility of adding a comment to the PDB
>> remark 2 which we have not used.
>> http://www.wwpdb.org/documentation/format33/remarks1.html#REMARK%202
>> This should help convince reviewers that you are not trying
>> to mis-represent the resolution of the structure.
>> 
>> 
>> Regards,
>> Mitch
>> 
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Edward A. Berry
>> Sent: Friday, December 07, 2012 8:43 AM
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] refining against weak data and Table I stats
>> 
>> Yes, well, actually i'm only a middle author on that paper for a good
>> reason, but I did encourage Rebecca and Stephan to use all the data.
>> But on a later, much more modest submission, where the outer shell
>> was not only weak but very incomplete (edges of the detector),
>> the reviewers found it difficult to evaluate the quality
>> of the data (we had also excluded a zone with bad ice-ring
>> problems). So we provided a second table, cutting off above
>> the ice ring in the good strong data, which convinced them
>> that at least it is a decent 2A structure. In the PDB it is
>> a 1.6A structure. but there was a lot of good data between
>> the ice ring and 1.6 A.
>> 
>> Bart Hazes (I think) suggested a statistic called "effective
>> resolution" which is the resolution to which a complete dataset
>> would have the number of reflectionin your dataset, and we
>> reported this, which came out to something like 1.75.
>> 
>> I do like the idea of reporting in multiple shells, not just overall
>> and highest shell, and the PDB accomodatesthis, even has a GUI
>> to enter it in the ADIT 2.0 software. It could also be used to
>> report two different overall ranges, such as completeness, 25 to 1.6 A,
>> which would be shocking in my case, and 25 to 2.0 which would
>> be more reassuring.
>> 
>> eab
>> 
>> Douglas Theobald wrote:
>>> Hi Ed,
>>> 
>>> Thanks for the comments.  So what do you recommend?  Refine against weak data, and report all stats in a single Table I?
>>> 
>>> Looking at your latest V-ATPase structure paper, it appears you favor something like that, since you report a high res shell with I/sigI=1.34 and Rsym=1.65.
>>> 
>>> 
>>> On Dec 6, 2012, at 7:24 PM, Edward A. Berry<[log in to unmask]>  wrote:
>>> 
>>>> Another consideration here is your PDB deposition. If the reason for using
>>>> weak data is to get a better structure, presumably you are going to deposit
>>>> the structure using all the data. Then the statistics in the PDB file must
>>>> reflect the high resolution refinement.
>>>> 
>>>> There are I think three places in the PDB file where the resolution is stated,
>>>> but i believe they are all required to be the same and to be equal to the
>>>> highest resolution data used (even if there were only two reflections in that shell).
>>>> Rmerge or Rsymm must be reported, and until recently I think they were not allowed
>>>> to exceed 1.00 (100% error?).
>>>> 
>>>> What are your reviewers going to think if the title of your paper is
>>>> "structure of protein A at 2.1 A resolution" but they check the PDB file
>>>> and the resolution was really 1.9 A?  And Rsymm in the PDB is 0.99 but
>>>> in your table 1* says 1.3?
>>>> 
>>>> Douglas Theobald wrote:
>>>>> Hello all,
>>>>> 
>>>>> I've followed with interest the discussions here about how we should be refining against weak data, e.g. data with I/sigI<<   2 (perhaps using all bins that have a "significant" CC1/2 per Karplus and Diederichs 2012).  This all makes statistical sense to me, but now I am wondering how I should report data and model stats in Table I.
>>>>> 
>>>>> Here's what I've come up with: report two Table I's.  For comparability to legacy structure stats, report a "classic" Table I, where I call the resolution whatever bin I/sigI=2.  Use that as my "high res" bin, with high res bin stats reported in parentheses after global stats.   Then have another Table (maybe Table I* in supplementary material?) where I report stats for the whole dataset, including the weak data I used in refinement.  In both tables report CC1/2 and Rmeas.
>>>>> 
>>>>> This way, I don't redefine the (mostly) conventional usage of "resolution", my Table I can be compared to precedent, I report stats for all the data and for the model against all data, and I take advantage of the information in the weak data during refinement.
>>>>> 
>>>>> Thoughts?
>>>>> 
>>>>> Douglas
>>>>> 
>>>>> 
>>>>> ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`
>>>>> Douglas L. Theobald
>>>>> Assistant Professor
>>>>> Department of Biochemistry
>>>>> Brandeis University
>>>>> Waltham, MA  02454-9110
>>>>> 
>>>>> [log in to unmask]
>>>>> http://theobald.brandeis.edu/
>>>>> 
>>>>>              ^\
>>>>>    /`  /^.  / /\
>>>>>   / / /`/  / . /`
>>>>> / /  '   '
>>>>> '
>>>>> 
>>>>> 

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