<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Jianghai,<br>
<br>
I'm confused about what you're comparing with what. Could you please
try this:<br>
<br>
1) Take a model;<br>
<br>
2) Run phenix.refine with it:<br>
<br>
% phenix.refine model.pdb data.mtz main.number_of_macro_cycles=0
strategy=none<br>
<br>
3) Run phenix.pdbtools with it:<br>
<br>
% phenix.pdbtools model.pdb --show-geometry-statistics<br>
<br>
Is the geometry statistics reported by phenix.refine and
phenix.pdbtools different? If it is different then there is a problem
and to fix it I will need to look at that PDB file.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 2/21/2008 5:19 PM, Jianghai Zhu wrote:
<blockquote
cite="mid:723CE5EF-067F-4350-8762-98E1D4C9ED1A@cbr.med.harvard.edu"
type="cite">
<div apple-content-edited="true"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<div style=""><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;">
<div style=""><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;">
<div>Here are the results.</div>
<div><br class="webkit-block-placeholder">
</div>
<div>phenix.pdbtools, riding H in the model.</div>
<div><br class="webkit-block-placeholder">
</div>
<div> |<font class="Apple-style-span" face="Courier">-Geometry
statistics---------------------------------------------------------|</font></div>
<div><font class="Apple-style-span" face="Courier">| Type |
Count | Deviation from ideal | Targets | Target (sum) |</font></div>
<div><font class="Apple-style-span" face="Courier">| |
| rmsd max min | | |</font></div>
<div><font class="Apple-style-span" face="Courier">| bond |
99522 | 0.004 0.085 0.000 | 0.028 | |</font></div>
<div><font class="Apple-style-span" face="Courier">| angle |
179035 | 0.793 21.106 0.000 | 0.099 | |</font></div>
<div><font class="Apple-style-span" face="Courier">| chirality |
7686 | 0.126 4.889 0.000 | 0.396 | 0.060 |</font></div>
<div><font class="Apple-style-span" face="Courier">| planarity |
15814 | 0.004 0.089 0.000 | 0.060 | |</font></div>
<div><font class="Apple-style-span" face="Courier">| dihedral |
24985 | 15.478 87.363 0.000 | 1.129 | |</font></div>
<div><font class="Apple-style-span" face="Courier">| nonbonded |
99522 | 3.939 4.900 1.125 | 0.725 | |</font></div>
<div><font class="Apple-style-span" face="Courier">|-----------------------------------------------------------------------------|</font></div>
<div><font class="Apple-style-span" face="Courier"><br
class="webkit-block-placeholder">
</font></div>
</span></span></span></span></span></span></div>
</span></div>
</span>phenix.pdbtools, without H in the model. </div>
<div apple-content-edited="true"><br class="webkit-block-placeholder">
</div>
<div apple-content-edited="true">
<div><font class="Apple-style-span" face="Courier">|-Geometry
statistics---------------------------------------------------------|</font></div>
<div><font class="Apple-style-span" face="Courier">| Type |
Count | Deviation from ideal | Targets | Target (sum) |</font></div>
<div><font class="Apple-style-span" face="Courier">| |
| rmsd max min | | |</font></div>
<div><font class="Apple-style-span" face="Courier">| bond |
51167 | 0.005 0.085 0.000 | 0.054 | |</font></div>
<div><font class="Apple-style-span" face="Courier">| angle |
69163 | 1.030 21.106 0.000 | 0.194 | |</font></div>
<div><font class="Apple-style-span" face="Courier">| chirality |
7686 | 0.126 4.889 0.000 | 0.396 | 0.142 |</font></div>
<div><font class="Apple-style-span" face="Courier">| planarity |
9110 | 0.005 0.089 0.000 | 0.104 | |</font></div>
<div><font class="Apple-style-span" face="Courier">| dihedral |
18756 | 17.864 87.363 0.000 | 1.504 | |</font></div>
<div><font class="Apple-style-span" face="Courier">| nonbonded |
51167 | 4.092 4.900 1.434 | 0.639 | |</font></div>
<div><font class="Apple-style-span" face="Courier">|-----------------------------------------------------------------------------|</font></div>
<div><br class="webkit-block-placeholder">
</div>
<div>phenix.refine reports at the end of the refinement with riding H.</div>
<div><br class="webkit-block-placeholder">
</div>
<div>
<div><font class="Apple-style-span" face="Courier"> stage angl
bond chir dihe plan repu geom_target</font></div>
<div><font class="Apple-style-span" face="Courier"> 0 : 1.394
0.124 0.147 20.782 0.004 3.925 1.1922e+00</font></div>
<div><font class="Apple-style-span" face="Courier">...</font></div>
<div><font class="Apple-style-span" face="Courier"> 6_bss: 0.622
0.011 0.120 13.143 0.003 3.822 2.6112e-02</font></div>
<div><br>
</div>
<div><br class="webkit-block-placeholder">
</div>
</div>
</div>
<div apple-content-edited="true">They are all different.</div>
<div apple-content-edited="true"><br class="webkit-block-placeholder">
</div>
<div apple-content-edited="true">Jianghai</div>
<br>
<div>
<div>On Feb 21, 2008, at 6:01 PM, Pavel Afonine wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"><br>
<blockquote type="cite">Is it possible that phenix.pdbtools ignored
the H atoms when <br>
</blockquote>
<blockquote type="cite">calculating the geometry statistics?<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<br>
Currently no. But you can easily do it in two steps:<br>
<br>
1) phenix.pdbtools model.pdb remove="element H" <br>
output.file_name=model_noH.pdb<br>
<br>
2) phenix.pdbtools model_noH.pdb --show-geometry-statistics<br>
<br>
Pavel.<br>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a></blockquote>
</div>
<br>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
</body>
</html>