<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div><span></span></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6396">Dear Pavel,</div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6405"><br></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6510"><br></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6478" dir="ltr">I find some reasons for the high clash. If the protein part PDB is without H and the ATP PDB part has H, the final clash score will be high. But it seems cif does not permit ligand without H, am I right? If I add H to both the protein and ligand, the poor resolution (poorer than 4) may be does not like to have the H added. What is your opinion?</div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6479" dir="ltr"><br></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6467" dir="ltr">Will you please explain whether the phenix.real_space_refined pdb's clashing score is same with that of MolProbity? If same, then there may be something wrong with my phenix software, as for recently I have 2 proteins, with phenix.real_space_refine, the critical clashing score 20 level cannot be got (always higher than 20).</div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6480" dir="ltr"><br></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6481" dir="ltr">Best regards.</div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6556" dir="ltr"><br></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6477" dir="ltr"><br></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1444048259607_6476" dir="ltr">Smith<br><br></div> <div class="yahoo_quoted" id="yui_3_16_0_1_1444048259607_6466" style="display: block;"> <div id="yui_3_16_0_1_1444048259607_6465" style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div id="yui_3_16_0_1_1444048259607_6464" style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div id="yui_3_16_0_1_1444048259607_6463" dir="ltr"> <font face="Arial" size="2"> On Monday, October 5, 2015 2:52 PM, Smith Liu <smith_liu123@163.com> wrote:<br> </font> </div> <br><br> <div class="y_msg_container"><div id="yiv9474680573"><div><div style="color: rgb(0, 0, 0); line-height: 1.7; font-family: Arial; font-size: 14px;"><div>Dear All,</div><div><br clear="none"></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 clear="none"></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 clear="none"></div><div>Best regards.</div><div class="yiv9474680573yqt7371650215" id="yiv9474680573yqtfd98992"><div><br clear="none"></div><div><br clear="none"></div></div><div><div class="yiv9474680573yqt7371650215" id="yiv9474680573yqtfd98230">Smith</div><br clear="none"><br clear="none"><br clear="none"><br clear="none"><br clear="none"></div><div></div><div id="yiv9474680573divNeteaseMailCard"></div><div><br clear="none"></div><pre><br clear="none">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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