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</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks Pavel,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> So the default value for the poor_map_value_threshold is 1, which I assume is 1 sigma. So if the electron density for a putative water is less than 1 sigma in the 2mFo-DFc map OR if the calculated correlation coefficient is less than the poor_cc_threshold value (default 0.7), then the water is removed, right?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> For my own education, what would be the best way of calculating the correlation coefficient values for all the waters or ligands in a given model? What I want to do is get a sense for the relationship between electron density and correlation coefficient values for waters in my structure to understand how “strict” the default poor_cc_threshold value is and whether/how much I might want to raise it.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks for your help,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>-Andy<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] <b>On Behalf Of </b>Pavel Afonine<br><b>Sent:</b> Tuesday, January 04, 2011 5:35 PM<br><b>To:</b> phenixbb@phenix-online.org<br><b>Subject:</b> Re: [phenixbb] Filtering ordered solvent molecules based on secondary map<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Andy,<br><br><br><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> I’m looking for a description of how the “secondary_map_and_map_cc_filter” parameter operates. The default is set to be a 2mFobs-DFmodel, and I assume it’s calculating a correlation coefficient as the basis for filtering waters that are present in the mFobs-DFmodel maps (i.e. primary map) but not in the 2mFo-DFc map. However, I’d like to confirm my assumption is true and also learn whether the cutoff value for whether or not a putative water molecule gets culled can be changed. I haven’t found the information in the online documentation or the Phenixbb archives. </span><o:p></o:p></p><p class=MsoNormal style='margin-bottom:12.0pt'><br>yes, the second map, 2mFo-DFc is used to computed map CC (poor_cc_threshold). Also, it is used to filter waters by the absolute value of the 2mFo-DFc map computed at water oxygen center (poor_map_value_threshold).<br><br>The default values are good for most of cases (I hope).<br><br>Pavel.<br><br><o:p></o:p></p></div></body></html>