[phenixbb] R-factor expectations when translational pseudo symmetry is present

Pavel Afonine pafonine at lbl.gov
Tue Apr 17 12:33:51 PDT 2018


Hi Mark,

all true statements, in general.

These tools are not to label an outlier as 'wrong'. Instead, they are 
meant to alert a user of something unusual, prompt to pay a closer 
attention and eventually explain the oddity (as result of paying a 
closer attention).

Very much like in your example, if Polygon shows an outlier and you 
bring good arguments to explain it (such as peculiarity of the data -- 
anisotropy, I/sigma, Rmerge, etc) then it's great and you are good to go.

The most common use case for the Polygon is when someone uses a 
suboptimal refinement strategy, gets hugely unlikely refinement 
statistics (such as R=25 at 1A resolution) and that goes unnoticed and 
ends up in the data base. One of my favorite examples is 1eic (1.4A, 
Rw=20, Rf=25). Polygon instantly tells you this is highly unusual. 
Applying proper refinement protocol, I can trivially get Rw and Rf down 
to 14 and 17% (otherwise, I would not know if I can potentially do this!).

Using resolution as a guide is just because this is easy to grasp by 
most users. Clearly, something like effective resolution (that accounts 
for data completeness, for example) may potentially be better.. but if I 
say "2A resolution" most people will instantaneously know what I mean, 
while if I say "effective resolution is 2A" I will have to explain what 
I mean (and I'm sure not all will be patient enough to listen!).

All in all, I'd say Polygon is based on a collection of compromises and 
shortcuts to get something useful and easy to grasp quickly.

All the best,
Pavel

On 4/17/18 12:16, Mark A. White wrote:
> Pavel,
>
> I have an issue with the general use of these metrics as an "IQ score" 
> for protein structures.  They completely ignore the details of the 
> experimental data and use one value, the maximum resolution, to set 
> the Bar.  There are at least two reasons that this can be a poor 
> choice.  (1) Highly Anisotropic data may go to 2.8A along one cell 
> axis, but only to 3.4A for the other two. (2) The parameters used to 
> cut the data.  Previously and I/sigma~3 or an Rmerge~30% were 
> considered the limits of usable data.  Today many data sets use a 
> CC1/2>=0.5 as a cutoff, with will include significantly more high 
> resolution data and push the "Resolution" to a higher value.  In both 
> cases we are now comparing data sets with data to ~1 I/sigma to older 
> data sets with an cutoff I/sigma of ~ 3 - 5.  These are not meaningful 
> comparisons.  If the software were to define a comparative resolution 
> based on I/sigma, completeness, then these comparisons would be  more 
> meaningful.
>
> If you want to reexamine the use of a single 'factor' in evaluating 
> anything I can highly recommend Stephen Jay Gould's the Mismeasure of 
> Man.  We need to examine the assumptions that are made in the creation 
> of these metrics.
>
> -- 
> Yours sincerely,
>
> Mark A. White, Ph.D.
> Associate Professor of Biochemistry and Molecular Biology,
> Manager, Sealy Center for Structural Biology and Molecular Biophysics
> Macromolecular X-ray Laboratory,
> Basic Science Building, Room 6.658A
> University of Texas Medical Branch
> Galveston, TX 77555-0647
> mailto://[email protected]
> http://xray.utmb.edu
>
> QQ: "I suppose it is tempting, if the only tool you have is a hammer, 
> to treat everything as if it were a nail."
> - Abraham Maslow (1966)
>
> -----Original Message-----
> *From*: Pavel Afonine <pafonine at lbl.gov 
> <mailto:Pavel%20Afonine%20%3cpafonine at lbl.gov%3e>>
> *To*: Tanner, John J. <TannerJJ at missouri.edu 
> <mailto:%22Tanner,%20John%20J.%22%20%3cTannerJJ at missouri.edu%3e>>, 
> phenixbb at phenix-online.org <phenixbb at phenix-online.org 
> <mailto:%22phenixbb at phenix-online.org%22%20%3cphenixbb at phenix-online.org%3e>>
> *Subject*: Re: [phenixbb] R-factor expectations when translational 
> pseudo symmetry is present
> *Date*: Fri, 13 Apr 2018 11:11:59 -0700
>
> Hi Jack,
>
> Polygon tool is designed answer questions like "what Rwork, Rfree and 
> Rfree-Rwork I expect at this resolution?".
> If focusing on R-factors only, then you can get a quick idea using a 
> command line tool:
>
> phenix.r_factor_statistics 2.25
>
> Histogram of Rwork for models in PDB at resolution 2.15-2.35 A:
>      0.123 - 0.144      : 36
>      0.144 - 0.165      : 442
>      0.165 - 0.187      : 1669
>      0.187 - 0.208      : 2782
> *0.208 - 0.230      : 2023 <<< Your case*
> *     0.230 - 0.251      : 812*
>      0.251 - 0.273      : 165
>      0.273 - 0.294      : 19
>      0.294 - 0.316      : 5
>      0.316 - 0.337      : 3
> Histogram of Rfree for models in PDB at resolution 2.15-2.35 A:
>      0.160 - 0.183      : 43
>      0.183 - 0.207      : 405
>      0.207 - 0.231      : 1485
>      0.231 - 0.255      : 2759
> *     0.255 - 0.278      : 2216 <<< Your case*
>      0.278 - 0.302      : 861
>      0.302 - 0.326      : 142
>      0.326 - 0.350      : 36
>      0.350 - 0.373      : 7
>      0.373 - 0.397      : 2
> Histogram of Rfree-Rwork for all model in PDB at resolution 2.15-2.35 A:
>      0.001 - 0.011      : 55
>      0.011 - 0.021      : 247
>      0.021 - 0.031      : 782
>      0.031 - 0.041      : 1597
> *     0.041 - 0.050      : 2124 <<< Your case*
>      0.050 - 0.060      : 1716
>      0.060 - 0.070      : 912
>      0.070 - 0.080      : 316
>      0.080 - 0.090      : 131
>      0.090 - 0.100      : 76
> Number of structures considered: 7956
>
> So it looks like R-factors you have is what one would expect at this 
> resolution.
>
> Pavel
>
> On 4/12/18 18:38, Tanner, John J. wrote:
>
>> Dear PhenixBB, 
>>
>>
>> We have a crystal form that xtriage flags as having strong 
>> translational pseudo symmetry (Patterson peak 57% the height of the 
>> origin peak, p-value = 3E-5). 
>>
>>
>> The space group is P21212. We can solve the structure with MR and 
>> refine to R=0.233 and R-free =0.276 at 2.25 Angstrom resolution. The 
>> maps look very good, but do not suggest major additional modeling 
>> that could be done to improve the structure and lower the R-factors. 
>> I know that one expects the R-factors from refinement to be higher 
>> when TPS is present, but my question is how high is too high?  Has 
>> anyone done a study that shows the expectations for R-factors when 
>> TPS is present? 
>>
>>
>> Thanks, 
>>
>>
>> Jack 
>>
>> John J. Tanner
>> Interim Chair, Department of Biochemistry 
>> Professor of Biochemistry and Chemistry 
>> Department of Biochemistry 
>> University of Missouri-Columbia
>> 117 Schweitzer Hall 
>> 503 S College Avenue
>> Columbia, MO 65211
>> Phone: 573-884-1280 
>> Fax: 573-882-5635
>> Email: tannerjj at missouri.edu <mailto:tannerjj at missouri.edu>
>> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html 
>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffaculty.missouri.edu%2F%257Etannerjj%2Ftannergroup%2Ftanner.html&data=02%7C01%7Cmawhite%40utmb.edu%7C4389508070e8473b2ea708d5a16a2022%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C636592399538790326&sdata=1SiH0MMgyycxtsLmsLDhHsXLYS1XSYs%2BJ6mJuUg0D1Y%3D&reserved=0> 
>
>> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C 
>> Office: Schlundt Annex 203A 
>>
>>
>>
>>
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