<div dir="ltr">Smith<div><br></div><div>From the comments in the file, you generated the ATP restraints with 1.9-1692. I redid the command with 1.10-2155 and the restraints were better. Clearly, the program has improved in the 13 months that 1.9 was released and you should stop using it in preference for 1.10.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Mon, Oct 5, 2015 at 3:31 AM, Smith Liu <span dir="ltr"><<a href="mailto:smith_liu123@163.com" target="_blank">smith_liu123@163.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><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><span class="HOEnZb"><font color="#888888"><div><br></div><div>Smith<br><br><br><br><br></div></font></span><div><div class="h5"><div></div><div></div><div><br></div>At 2015-10-05 14:12:39, "Pavel Afonine" <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>> wrote:<br> <blockquote 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>On 10/4/15 21:51, Smith Liu wrote:<br>
</div>
<blockquote 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 href="mailto:pafonine@lbl.gov" target="_blank"><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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