<!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">
Qun<br>
<br>
Two things. I think you will find a large group of people who will
disagree with your assertion that your refinement should not contain
hydrogens. Secondly, can you tell me which version your are using? Is
it 1.4-3?<br>
<br>
Nigel<br>
<br>
On 3/19/09 4:21 PM, crystallogrphy wrote:
<blockquote
cite="mid:33fd30c80903191621u7fa5c3ddpcabc7c422bc54c58@mail.gmail.com"
type="cite"><br clear="all">
Hi, <br>
I am using phenix.elbow to generate pdb and cif files with the tripos
format file:<br>
<meta http-equiv="CONTENT-TYPE" content="text/html; ">
<title></title>
<meta name="GENERATOR" content="OpenOffice.org 2.0 (Unix)">
<meta name="AUTHOR" content="qun_wan">
<meta name="CREATED" content="20090318;14212000">
<meta name="CHANGEDBY" content="qun_wan">
<meta name="CHANGED" content="20090319;20070300">
<style>
<!--
@page { size: 8.5in 11in; margin: 0.79in }
P { margin-bottom: 0.08in }
-->
</style>
<ol start="5">
<p style="margin-bottom: 0in;">phenix.elbow --initial_geometry
egcg.mol2 --opt --output="LIG" --pdb-ligand</p>
</ol>
The input pdb file contains hydrogen atoms and the output pdb file also
contains hydrogen atom. 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>
<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8">
<title></title>
<meta name="GENERATOR" content="OpenOffice.org 2.0 (Unix)">
<meta name="AUTHOR" content="qun_wan">
<meta name="CREATED" content="20090318;14212000">
<meta name="CHANGEDBY" content="qun_wan">
<meta name="CHANGED" content="20090319;20070300">
<style>
<!--
@page { size: 8.5in 11in; margin: 0.79in }
P { margin-bottom: 0.08in }
-->
</style>
<ol start="5">
<p style="margin-bottom: 0in;">phenix.elbow --initial_geometry
--write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand</p>
</ol>
<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>
<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>
<br>
<pre class="moz-signature" cols="72">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov</pre>
</body>
</html>