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</o:shapelayout></xml><![endif]--></head><body lang=EL link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Hi Havier,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>You got the formula right <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>You may have also some water include in the model correspond to alternate loop A" occupancy = X <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>I have done it many times using RefMac and SHELX I am sure it is working in Phenix as well .<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>you do not need something specific in a parameter file for the protein atom.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>The PDB file look like the following.<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-GB style='font-size:11.0pt;font-family:"Courier New"'>ATOM 258 CA <span style='background:yellow;mso-highlight:yellow'>A</span>GLN A 35 2.979 -4.265 69.678 0.40 46.35 C<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-GB style='font-size:11.0pt;font-family:"Courier New"'>ANISOU 258 CA <span style='background:yellow;mso-highlight:yellow'>A</span>GLN A 35 4942 7133 5533 0 946 -219 C<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-GB style='font-size:11.0pt;font-family:"Courier New"'>ATOM 259 CA <span style='background:yellow;mso-highlight:yellow'>B</span>GLN A 35 3.127 -4.246 69.643 0.60 47.74 C<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-GB style='font-size:11.0pt;font-family:"Courier New"'>ANISOU 259 CA <span style='background:yellow;mso-highlight:yellow'>B</span>GLN A 35 5152 7285 5702 0 930 -219 C<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>The alternative atom specified with letter A and B before the amino acid three letters.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Regards,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>George<o:p></o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri",sans-serif'> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] <b>On Behalf Of </b>Xavier Brazzolotto<br><b>Sent:</b> Tuesday, July 24, 2018 9:50 AM<br><b>To:</b> phenixbb@phenix-online.org<br><b>Subject:</b> [phenixbb] Ligand occupancy and conformational change<o:p></o:p></span></p></div></div><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal><span style='color:black'>I am struggling with a ligand bound structure.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Hope I did myself clear.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>How to deal with this situation ? I am sure that phenix.refine can do it but how ?<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Maybe something specific in a parameter file ?<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Thank you for your help<o:p></o:p></span></p></div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal><span style='color:black'>Xavier<o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></body></html>