<div dir="ltr">I don't get this. Are you doing small molecule crystallography with phenix.refine? <br>Or are you using CdCl2 as a cover for a secret ligand? Because CdCl2 is highly water soluble. There shouldn't be a three-letter code for it. <div><br></div></div><br><div class="gmail_quote">On Wed, Apr 8, 2015 at 4:39 AM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
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.</div><div bgcolor="#FFFFFF" text="#000000"><br>
<br>
Pavel</div><div bgcolor="#FFFFFF" text="#000000"><br>
<br>
<div>On 4/6/15 10:06 AM, Tarek DawoD wrote:<br>
</div>
<blockquote type="cite">
<div style="color:#000;background-color:#fff;font-family:HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif;font-size:16px">
<div dir="ltr"><br>
Dear All</div>
<div dir="ltr"><br>
</div>
<div dir="ltr">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 dir="ltr">i could not find 3 letter could for CdCl2.</div>
<div dir="ltr"><br>
</div>
<div>COMPND UNNAMED
</div>
<div>AUTHOR GENERATED BY OPEN BABEL 2.3.1
</div>
<div>HETATM 1 CD LIG 1 0.994 8.428
20.546 1.00 0.00 Cd </div>
<div>HETATM 2 CL1 LIG 1 -0.441 6.507
20.373 1.00 0.00 Cl </div>
<div>HETATM 3 CL2 LIG 1 3.190 7.731
21.231 1.00 0.00 Cl </div>
<div>END</div>
<div><br>
</div>
<div dir="ltr">Thank you for Help.</div>
<div dir="ltr">regards</div>
<div dir="ltr">TK_DawoD</div>
<div><br>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
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