<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><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 style="position: relative; -ms-zoom: 1;"></div><div id="divNeteaseMailCard"></div><div><br></div><pre><br>At 2015-10-05 02:14:28, "Pavel Afonine" <pafonine@lbl.gov> 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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