Hi,there<br>I found that the cif file of ligand from ProDRG server is not good for phenix.refine.<br>I always got my ligand pdb file using ProDRG, and use the refmac file as the restraint file of the ligand, but I found that after running the phenix.refine, the rmsANGLE is very high.<br>
the I followed someone&#39;s advice, using phenix.elbow to produce the ligand&#39;s cif file, that really make sense, now I can easily get the refinement value of the complex structure in a <br>reasonable level.<br>Hope it works with your structure too.<br>
<br>Tiantian<br><br><div class="gmail_quote">On Tue, May 24, 2011 at 3:34 PM, Priit Eek <span dir="ltr">&lt;<a href="mailto:priit.eek@gmail.com">priit.eek@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks Nigel and Yuri! elbow.where_is_that_cif_file gave me the right cif to use in coot. Off to fix that sucrose now...<br>
<font color="#888888"><br>
Priit<br>
</font><div><div></div><div class="h5"><br>
<br>
On 23.05.2011, at 17:55, Yuri wrote:<br>
<br>
&gt; All coot needs to run its real-space refinement is a .cif file as Nigel pointed out.<br>
&gt; You can also get this file from other ligand library websites (proDrg, hic-cup, etc...). The only catch here is. The name of your sucrose atoms must match, exactly, those in the file.<br>
&gt; Once you have such file go to the the file drop-down menu and click on Import CIF dictionary in coot. That should enable to rotate the rotatable bonds of your ligand<br>
&gt;<br>
&gt; --<br>
&gt; Yuri Pompeu<br>
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