<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Dear Pavel,</div><div><br></div><div>My cif file was for ATP, which was rather easily got by eLBOW as for the Phenix contains it in its library. Attached is the ATP.cif file I used.</div><div><br></div><div>In addition, I have run another 10 cycles of simulated_annealing+minimization_global, and the clash score was still 120 (too high).</div><div><br></div><div>Recently I fond for both the 1.9-1692 and 1.10.2155 version of phenix.real_spacea_refine, I got rather high clash score (higher than 20). In addition I found (recently?) the phenix.real_space_refine output PDB clash score was different from the Ramachandran clash score value. Is an possibility my Windows versions of phenix have something wrong?</div><div><br></div><div>I am looking forward to getting your further comment.</div><div><br></div><div>Smith<br><br><br><br><br></div><div style="position: relative; -ms-zoom: 1;"></div><div id="divNeteaseMailCard"></div><div><br></div>At 2015-10-05 14:12:39, "Pavel Afonine" <pafonine@lbl.gov> wrote:<br> <blockquote id="isReplyContent" style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left-color: rgb(204, 204, 204); border-left-width: 1px; border-left-style: solid;">
Most likely wrong ligand CIF file.<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 10/4/15 21:51, Smith Liu wrote:<br>
</div>
<blockquote cite="mid:3b1997f3.57d9.1503657158a.Coremail.smith_liu123@163.com" type="cite">
<div style="color: rgb(0, 0, 0); line-height: 1.7; font-family: Arial; font-size: 14px;">
<div>Dear All,</div>
<div><br>
</div>
<div>I have tried a phenix.real_space_refine with a ligand cif
and without ligand cif (both with ligand PDB in the whole
protein-ligand PDB for refine), I find with ligand cif in the
input can lead to significant increase of the clash score for
the refined PDB.</div>
<div><br>
</div>
<div>Will you please make comment on whether the clash score
incensement by adding cif in the input was a general
phenomenon, or only specific to my situation, and how to solve
it?</div>
<div><br>
</div>
<div>Best regards.</div>
<div><br>
</div>
<div><br>
</div>
<div>Smith<br>
<br>
<br>
<br>
<br>
</div>
<div><br>
</div>
<pre>At 2015-10-05 02:14:28, "Pavel Afonine" <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a> wrote:
>Yes.
>Pavel
>
>On 10/4/15 02:19, Smith Lee wrote:
>> Dear All,
>>
>> Does phenix.refine can process some ligands without the process by eLBOW, for example ATP, ADP,etc?
>>
>>
>> Smith
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