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In the absence of expert reply, my naive suggestion is: just make a
3-letter code up using elbow.get_new_ligand_code command-line tool.
I can see this as three steps:<br>
<br>
- run elbow.get_new_ligand_code to get 3-letter code;<br>
- edit ligand PDB file to replace LIG with the new code;<br>
- run elbow with the new PDB file.<br>
<br>
Note, PDB file is a poor file to specify chemistry, use SMILES
strings if possible instead.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 4/6/15 10:06 AM, Tarek DawoD wrote:<br>
</div>
<blockquote
cite="mid:231119833.374534.1428340011704.JavaMail.yahoo@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
dir="ltr" style=""><br class="" style="">
Dear All</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
dir="ltr" style=""><br class="" style="">
</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
dir="ltr" style="">if i have pdb file for CdCl2, how could i
generate cif file (to use later in phenix.refine) from that
using readyset or elbow or any other tool.</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
dir="ltr" style="">i could not find 3 letter could for CdCl2.</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
dir="ltr" style=""><br class="" style="">
</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
style="">COMPND � �UNNAMED � � � � � � � � � � � � � � � � � �
� � � � � � � � � � � � ��</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
style="">AUTHOR � �GENERATED BY OPEN BABEL 2.3.1 � � � � � � �
� � � � � � � � � � � � ��</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
style="">HETATM � �1 CD � LIG � � 1 � � � 0.994 � 8.428
�20.546 �1.00 �0.00 � � � � �Cd �</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
style="">HETATM � �2 CL1 �LIG � � 1 � � �-0.441 � 6.507
�20.373 �1.00 �0.00 � � � � �Cl �</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
style="">HETATM � �3 CL2 �LIG � � 1 � � � 3.190 � 7.731
�21.231 �1.00 �0.00 � � � � �Cl �</div>
<div id="yiv8842103088yui_3_16_0_1_1428338803661_6715" class=""
style="">END</div>
<div class="" id="yiv8842103088yui_3_16_0_1_1428338803661_6789"
style=""><br class="" style="">
</div>
<div class="" id="yiv8842103088yui_3_16_0_1_1428338803661_6789"
dir="ltr" style="">Thank you for Help.</div>
<div class="" id="yiv8842103088yui_3_16_0_1_1428338803661_6789"
dir="ltr" style="">regards</div>
<div class="" id="yiv8842103088yui_3_16_0_1_1428338803661_6789"
dir="ltr" style="">TK_DawoD</div>
<div id="yui_3_16_0_1_1428338803661_43618" class="" style=""><br
class="" style="">
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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