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Hi Mark,<br>
<br>
all true statements, in general. <br>
<br>
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).<br>
<br>
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.<br>
<br>
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!). <br>
<br>
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!).<br>
<br>
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.<br>
<br>
All the best,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 4/17/18 12:16, Mark A. White wrote:<br>
</div>
<blockquote type="cite"
cite="mid:1523992593.8556.804.camel@marvin.utmb.edu">
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Pavel,<br>
<br>
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.<br>
<br>
<font color="#000000">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.</font><br>
<br>
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-- <br>
Yours sincerely, <br>
<br>
Mark A. White, Ph.D. <br>
Associate Professor of Biochemistry and Molecular Biology,
<br>
Manager, Sealy Center for Structural Biology and Molecular
Biophysics <br>
Macromolecular X-ray Laboratory, <br>
Basic Science Building, Room 6.658A <br>
University of Texas Medical Branch <br>
Galveston, TX 77555-0647 <br>
<a class="moz-txt-link-freetext" href="mailto://mawhite@utmb.edu">mailto://mawhite@utmb.edu</a> <br>
<a class="moz-txt-link-freetext" href="http://xray.utmb.edu">http://xray.utmb.edu</a> <br>
<br>
QQ: "I suppose it is tempting, if the only tool you have
is a hammer, to treat everything as if it were a nail." <br>
- Abraham Maslow (1966) <br>
<br>
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-----Original Message-----<br>
<b>From</b>: Pavel Afonine <<a
href="mailto:Pavel%20Afonine%20%3cpafonine@lbl.gov%3e"
moz-do-not-send="true">pafonine@lbl.gov</a>><br>
<b>To</b>: Tanner, John J. <<a
href="mailto:%22Tanner,%20John%20J.%22%20%3cTannerJJ@missouri.edu%3e"
moz-do-not-send="true">TannerJJ@missouri.edu</a>>,
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a> <<a
href="mailto:%22phenixbb@phenix-online.org%22%20%3cphenixbb@phenix-online.org%3e"
moz-do-not-send="true">phenixbb@phenix-online.org</a>><br>
<b>Subject</b>: Re: [phenixbb] R-factor expectations when
translational pseudo symmetry is present<br>
<b>Date</b>: Fri, 13 Apr 2018 11:11:59 -0700<br>
<br>
Hi Jack,<br>
<br>
Polygon tool is designed answer questions like "what Rwork, Rfree
and Rfree-Rwork I expect at this resolution?". <br>
If focusing on R-factors only, then you can get a quick idea using
a command line tool:<br>
<br>
<tt>phenix.r_factor_statistics 2.25</tt><br>
<br>
<tt>Histogram of Rwork for models in PDB at resolution 2.15-2.35
A:</tt><br>
<tt> 0.123 - 0.144 : 36</tt><br>
<tt> 0.144 - 0.165 : 442</tt><br>
<tt> 0.165 - 0.187 : 1669</tt><br>
<tt> 0.187 - 0.208 : 2782</tt><br>
<tt> </tt><tt><b>0.208 - 0.230 : 2023 <<< Your
case</b></tt><br>
<b><tt> 0.230 - 0.251 : 812</tt></b><br>
<tt> 0.251 - 0.273 : 165</tt><br>
<tt> 0.273 - 0.294 : 19</tt><br>
<tt> 0.294 - 0.316 : 5</tt><br>
<tt> 0.316 - 0.337 : 3</tt><br>
<tt>Histogram of Rfree for models in PDB at resolution 2.15-2.35
A:</tt><br>
<tt> 0.160 - 0.183 : 43</tt><br>
<tt> 0.183 - 0.207 : 405</tt><br>
<tt> 0.207 - 0.231 : 1485</tt><br>
<tt> 0.231 - 0.255 : 2759</tt><br>
<b><tt> 0.255 - 0.278 : 2216 <<< Your case</tt></b><br>
<tt> 0.278 - 0.302 : 861</tt><br>
<tt> 0.302 - 0.326 : 142</tt><br>
<tt> 0.326 - 0.350 : 36</tt><br>
<tt> 0.350 - 0.373 : 7</tt><br>
<tt> 0.373 - 0.397 : 2</tt><br>
<tt>Histogram of Rfree-Rwork for all model in PDB at resolution
2.15-2.35 A:</tt><br>
<tt> 0.001 - 0.011 : 55</tt><br>
<tt> 0.011 - 0.021 : 247</tt><br>
<tt> 0.021 - 0.031 : 782</tt><br>
<tt> 0.031 - 0.041 : 1597</tt><br>
<b><tt> 0.041 - 0.050 : 2124 <<< Your case</tt></b><br>
<tt> 0.050 - 0.060 : 1716</tt><br>
<tt> 0.060 - 0.070 : 912</tt><br>
<tt> 0.070 - 0.080 : 316</tt><br>
<tt> 0.080 - 0.090 : 131</tt><br>
<tt> 0.090 - 0.100 : 76</tt><br>
<tt>Number of structures considered: 7956</tt><br>
<br>
So it looks like R-factors you have is what one would expect at
this resolution.<br>
<br>
Pavel<br>
<br>
On 4/12/18 18:38, Tanner, John J. wrote:<br>
<br>
<blockquote type="CITE"> Dear PhenixBB, </blockquote>
<blockquote type="CITE"> <br>
<br>
</blockquote>
<blockquote type="CITE"> 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). </blockquote>
<blockquote type="CITE"> <br>
<br>
</blockquote>
<blockquote type="CITE"> 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?
</blockquote>
<blockquote type="CITE"> <br>
<br>
</blockquote>
<blockquote type="CITE"> Thanks,
</blockquote>
<blockquote type="CITE"> <br>
<br>
</blockquote>
<blockquote type="CITE"> Jack
</blockquote>
<blockquote type="CITE"> <br>
</blockquote>
<blockquote type="CITE"> John J. Tanner<br>
Interim Chair, Department of Biochemistry
</blockquote>
<blockquote type="CITE"> Professor of Biochemistry and Chemistry
</blockquote>
<blockquote type="CITE"> Department of Biochemistry
</blockquote>
<blockquote type="CITE"> University of Missouri-Columbia<br>
117 Schweitzer Hall
</blockquote>
<blockquote type="CITE"> 503 S College Avenue<br>
Columbia, MO 65211<br>
Phone: 573-884-1280
</blockquote>
<blockquote type="CITE"> Fax: 573-882-5635<br>
Email: <a href="mailto:tannerjj@missouri.edu"
moz-do-not-send="true">tannerjj@missouri.edu</a><br>
<a
href="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"
moz-do-not-send="true">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a>
</blockquote>
<blockquote type="CITE"> Lab: Schlundt Annex rooms 3,6,9, 203B,
203C
</blockquote>
<blockquote type="CITE"> Office: Schlundt Annex 203A
</blockquote>
<blockquote type="CITE"> <br>
<br>
</blockquote>
<blockquote type="CITE"> <br>
<br>
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