Please ignore “(see attached png file)” in my previous post.
Sent from Jack's iPhone
On Apr 14, 2018, at 7:49 AM, Tanner, John J. mailto:[email protected]> wrote:
Thanks Pavel for the advice on polygon. I ran polygon using the phenix GUI. According to the GUI, my R-factors are on the edge of the histogram:
https://www.dropbox.com/s/txq7pmu1xrjmjb7/polygon.png?dl=0
It seems like the R-factor histograms from the GUI are different from those generated by phenix.r_factor_statistics (see attached png file).
Also, what is the difference in the GUI histograms for R-work and R-work (PDB)?
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: [email protected]mailto:[email protected]
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A
On Apr 13, 2018, at 1:11 PM, Pavel Afonine mailto:[email protected]> wrote:
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: [email protected]mailto:[email protected]
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.htmlhttp://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A
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