[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://mawhite@utmb.edu
> 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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