<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class="">I am struggling with a ligand bound structure.</div><div class="">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.</div><div class=""><br class=""></div><div class="">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.</div><div class="">Hope I did myself clear.</div><div class=""><br class=""></div><div class="">How to deal with this situation ? I am sure that phenix.refine can do it but how ?</div><div class="">What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X</div><div class="">Maybe something specific in a parameter file ?</div><div class=""><br class=""></div><div class="">Thank you for your help</div><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="">Xavier</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></body></html>