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Hi Qun Wan,<br>
<br>
check out this:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/refinement.htm#anch28">http://www.phenix-online.org/documentation/refinement.htm#anch28</a><br>
<br>
and slide #37 here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/neutron_japan_2009/">http://www.phenix-online.org/presentations/neutron_japan_2009/</a><br>
-> Structure refinement and PHENIX (morning session) (PDF)<br>
<br>
this says some things about hydrogens in refinement. <br>
<br>
Pavel.<br>
<br>
<br>
<br>
<blockquote
cite="mid:33fd30c80903191621u7fa5c3ddpcabc7c422bc54c58@mail.gmail.com"
type="cite">My crystal data only difftracted to 2.4A, so hydrogen
atoms cannot be seen. In the refinement, my ligand should not contain
hydrogen atoms. So I add one more option not to add hydrogen following
the online phenix documentation:<br>
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<p style="margin-bottom: 0in;">phenix.elbow --initial_geometry
--write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand</p>
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<b>However, the program failed. Does anyone know why?</b><br>
Usage: phenix.elbow [options]<br>
<b>phenix.elbow: error: no such option: --write-hydrogens</b><br>
<br>
-- <br>
Qun Wan<br>
Department of Pharmacology, Case Western Reserve University<br>
10900 Euclid Avenue, Cleveland, OH 44106<br>
email: <a moz-do-not-send="true" href="mailto:qunwan1@gmail.com">qunwan1@gmail.com</a><br>
lab phone: 216-368-3337<br>
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