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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><tt><br>
</tt><tt><br>
</tt><tt>Histogram of Rwork for models in PDB at resolution
2.15-2.35 A:</tt><tt><br>
</tt><tt>���� 0.123 - 0.144����� : 36</tt><tt><br>
</tt><tt>���� 0.144 - 0.165����� : 442</tt><tt><br>
</tt><tt>���� 0.165 - 0.187����� : 1669</tt><tt><br>
</tt><tt>���� 0.187 - 0.208����� : 2782</tt><tt><br>
</tt><tt>���� <b>0.208 - 0.230����� : 2023</b></tt><b><tt>
<<< Your case<br>
</tt></b><b><tt>���� 0.230 - 0.251����� : 812</tt></b><tt><br>
</tt><tt>���� 0.251 - 0.273����� : 165</tt><tt><br>
</tt><tt>���� 0.273 - 0.294����� : 19</tt><tt><br>
</tt><tt>���� 0.294 - 0.316����� : 5</tt><tt><br>
</tt><tt>���� 0.316 - 0.337����� : 3</tt><tt><br>
</tt><tt>Histogram of Rfree for models in PDB at resolution
2.15-2.35 A:</tt><tt><br>
</tt><tt>���� 0.160 - 0.183����� : 43</tt><tt><br>
</tt><tt>���� 0.183 - 0.207����� : 405</tt><tt><br>
</tt><tt>���� 0.207 - 0.231����� : 1485</tt><tt><br>
</tt><tt>���� 0.231 - 0.255����� : 2759</tt><tt><br>
</tt><b><tt>���� 0.255 - 0.278����� : 2216</tt></b><tt><b>
<<< Your case</b><br>
</tt><tt>���� 0.278 - 0.302����� : 861</tt><tt><br>
</tt><tt>���� 0.302 - 0.326����� : 142</tt><tt><br>
</tt><tt>���� 0.326 - 0.350����� : 36</tt><tt><br>
</tt><tt>���� 0.350 - 0.373����� : 7</tt><tt><br>
</tt><tt>���� 0.373 - 0.397����� : 2</tt><tt><br>
</tt><tt>Histogram of Rfree-Rwork for all model in PDB at resolution
2.15-2.35 A:</tt><tt><br>
</tt><tt>���� 0.001 - 0.011����� : 55</tt><tt><br>
</tt><tt>���� 0.011 - 0.021����� : 247</tt><tt><br>
</tt><tt>���� 0.021 - 0.031����� : 782</tt><tt><br>
</tt><tt>���� 0.031 - 0.041����� : 1597</tt><tt><br>
</tt><b><tt>���� 0.041 - 0.050����� : 2124</tt></b><tt><b>
<<< Your case</b><br>
</tt><tt>���� 0.050 - 0.060����� : 1716</tt><tt><br>
</tt><tt>���� 0.060 - 0.070����� : 912</tt><tt><br>
</tt><tt>���� 0.070 - 0.080����� : 316</tt><tt><br>
</tt><tt>���� 0.080 - 0.090����� : 131</tt><tt><br>
</tt><tt>���� 0.090 - 0.100����� : 76</tt><tt><br>
</tt><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>
<div class="moz-cite-prefix">On 4/12/18 18:38, Tanner, John J.
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:1CBEEA6C-F632-4D04-9BAB-7E7F91528DFE@missouri.edu">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Dear PhenixBB,
<div class=""><br class="">
</div>
<div class="">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).�
<div class=""><br class="">
</div>
<div class="">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?�</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class=""><br class="">
</div>
<div class="">Jack�</div>
<div class=""><br class="">
<div class="">
<div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; word-wrap: break-word;
-webkit-nbsp-mode: space; -webkit-line-break:
after-white-space;" class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica;
font-style: normal; font-variant-ligatures: normal;
font-variant-caps: normal; font-variant-east-asian:
normal; font-variant-position: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-align: -webkit-auto; text-indent:
0px; text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; word-wrap: break-word;
-webkit-nbsp-mode: space; -webkit-line-break:
after-white-space;" class="">
<div style="orphans: 2; text-align: -webkit-auto;
text-indent: 0px; widows: 2; word-wrap: break-word;
-webkit-nbsp-mode: space; -webkit-line-break:
after-white-space;" class="">
<div style="orphans: 2; text-align: -webkit-auto;
text-indent: 0px; widows: 2; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div style="orphans: 2; text-align: -webkit-auto;
text-indent: 0px; widows: 2; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div style="orphans: 2; text-align:
-webkit-auto; text-indent: 0px; widows: 2;
word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space;"
class="">
<div style="orphans: 2; text-align:
-webkit-auto; text-indent: 0px; widows: 2;
word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break:
after-white-space;" class="">
<div style="orphans: 2; text-align:
-webkit-auto; text-indent: 0px; widows: 2;
word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break:
after-white-space;" class="">
<div style="color: rgb(0, 0, 0);
font-family: Helvetica; font-style:
normal; font-variant-ligatures: normal;
font-variant-caps: normal;
font-variant-east-asian: normal;
font-variant-position: normal;
font-weight: normal; letter-spacing:
normal; line-height: normal;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;"
class="">
John J. Tanner<br class="">
Interim Chair, Department of
Biochemistry�</div>
<div style="color: rgb(0, 0, 0);
font-family: Helvetica; font-style:
normal; font-variant-ligatures: normal;
font-variant-caps: normal;
font-variant-east-asian: normal;
font-variant-position: normal;
font-weight: normal; letter-spacing:
normal; line-height: normal;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;"
class="">
Professor of�Biochemistry�and�Chemistry</div>
<div style="color: rgb(0, 0, 0);
font-family: Helvetica; font-style:
normal; font-variant-ligatures: normal;
font-variant-caps: normal;
font-variant-east-asian: normal;
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font-weight: normal; letter-spacing:
normal; line-height: normal;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;"
class="">
<span style="text-align: -webkit-auto;"
class="">Department of Biochemistry</span></div>
<div style="color: rgb(0, 0, 0);
font-family: Helvetica; font-style:
normal; font-variant-ligatures: normal;
font-variant-caps: normal;
font-variant-east-asian: normal;
font-variant-position: normal;
font-weight: normal; letter-spacing:
normal; line-height: normal;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;"
class="">
University of Missouri-Columbia<br
class="">
117 Schweitzer Hall</div>
<div class="">503 S College Avenue<br
class="">
Columbia, MO 65211<br class="">
Phone: 573-884-1280</div>
<div style="color: rgb(0, 0, 0);
font-family: Helvetica; font-style:
normal; font-variant-ligatures: normal;
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normal; line-height: normal;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;"
class="">
Fax:�573-882-5635<br class="">
Email:�<a
href="mailto:tannerjj@missouri.edu"
class="" moz-do-not-send="true">tannerjj@missouri.edu</a><br
class="">
<a
href="http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html"
class="" moz-do-not-send="true">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a></div>
<div style="color: rgb(0, 0, 0);
font-family: Helvetica; font-style:
normal; font-variant-ligatures: normal;
font-variant-caps: normal;
font-variant-east-asian: normal;
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font-weight: normal; letter-spacing:
normal; line-height: normal;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;"
class="">
Lab: Schlundt Annex rooms 3,6,9, 203B,
203C</div>
<div style="color: rgb(0, 0, 0);
font-family: Helvetica; font-style:
normal; font-variant-ligatures: normal;
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font-weight: normal; letter-spacing:
normal; line-height: normal;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;"
class="">
Office:�Schlundt Annex 203A</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</div>
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<br>
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