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Now I see what you did. I tried exact same things myself using an
arbitrary structure from PDB. I couldn't reproduce your problem using
both: the current development code and the latest CCI Apps:
2008_02_08_1610. <br>
<br>
In this case I can only work on this problem if you send us the
reproducer so we can reproduce your problem.<br>
<br>
Pavel.<br>
<br>
<br>
On 2/21/2008 6:06 PM, Jianghai Zhu wrote:
<blockquote
cite="mid:385EEB2F-3D63-46A3-9D87-BB8DB9CF0484@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>Sorry, I should have made it clear.</div>
<div><br class="webkit-block-placeholder">
</div>
<div>I started a refinement using phenix.refine with riding H in my
model. After the refinement, I got the following at the end of the log
and the header of the pdb file.</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>
<div><br class="webkit-block-placeholder">
</div>
<div><br class="webkit-block-placeholder">
</div>
Using this refined model, I did phenix.pdbtools model.pdb
--show-geometry-statistics. And I got the following.</span></span></span></span></span></span></div>
<div style=""><br class="webkit-block-placeholder">
</div>
<div style="">
<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>
</div>
</span></div>
</span>Using this refined model, I did phenix.refine model.pdb
data.mtz main.number_of_macro_cycles=0 strategy=none. And I got the
following. </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">------------------------------------------------------------------------</font></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 : 0.608
0.003 0.120 12.395 0.003 3.928 2.9651e-02</font></div>
<div><font class="Apple-style-span" face="Courier">------------------------------------------------------------------------</font></div>
<div><br class="webkit-block-placeholder">
</div>
</div>
<div apple-content-edited="true">After removing the H from the
refined model, I did phenix.pdbtools model_noH.pdb
--show-geometry-statistics. And I got the following.</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>
<div apple-content-edited="true"><br class="webkit-block-placeholder">
</div>
<div apple-content-edited="true"><br class="webkit-block-placeholder">
</div>
<div apple-content-edited="true">Jianghai</div>
<div apple-content-edited="true"><br class="webkit-block-placeholder">
</div>
<div apple-content-edited="true"><br class="webkit-block-placeholder">
</div>
<div>
<div>On Feb 21, 2008, at 8:35 PM, Pavel Afonine wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div 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>
</div>
</blockquote>
</div>
<br>
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