<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Thanks George</div><div class=""><br class=""></div>The residues of the loops are already assigned with ARESNAME and BRESNAME and it is ok to refine both loops<div class=""><br class=""></div><div class=""><div class="">What I would like to do is then to add the ligand. But in the apo state it clashes with one residue of the loop.</div><div class="">So I thought fixing the occupancy to 0 (zero), for one ALT of the ligand (with apo loop) and having a second ALT with an occupancy <1 (bound loop) to try to prevent atom clashing.</div><div class="">Is it the right strategy ? And how to do it ?</div><div class=""><br class=""></div><div class="">Moreover, it seems to get more complicated as the bound ligand can also exist with at least 2 different alternatives (different orientation of a central indole ring).</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">Le 24 juil. 2018 à 09:49, G_Kontopidis <<a href="mailto:gkontopidis@vet.uth.gr" class="">gkontopidis@vet.uth.gr</a>> a écrit :</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi Havier,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">You got the formula right<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">You may have also some water include in the model correspond to alternate loop A" occupancy = X<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">I have done it many times using RefMac and SHELX I am sure it is working in Phenix as well .<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">you do not need something specific in a parameter file for the protein atom.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">The PDB file look like the following.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: "Courier New";" class="">ATOM 258 CA<span class="Apple-converted-space"> </span><span style="background-color: yellow; background-position: initial initial; background-repeat: initial initial;" class="">A</span>GLN A 35 2.979 -4.265 69.678 0.40 46.35 C<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: "Courier New";" class="">ANISOU 258 CA<span class="Apple-converted-space"> </span><span style="background-color: yellow; background-position: initial initial; background-repeat: initial initial;" class="">A</span>GLN A 35 4942 7133 5533 0 946 -219 C<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: "Courier New";" class="">ATOM 259 CA<span class="Apple-converted-space"> </span><span style="background-color: yellow; background-position: initial initial; background-repeat: initial initial;" class="">B</span>GLN A 35 3.127 -4.246 69.643 0.60 47.74 C<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: "Courier New";" class="">ANISOU 259 CA<span class="Apple-converted-space"> </span><span style="background-color: yellow; background-position: initial initial; background-repeat: initial initial;" class="">B</span>GLN A 35 5152 7285 5702 0 930 -219 C<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">The alternative atom specified with letter A and B before the amino acid three letters.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Regards,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">George<o:p class=""></o:p></span></div><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><b class=""><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span><a href="mailto:phenixbb-bounces@phenix-online.org" class="">phenixbb-bounces@phenix-online.org</a> [<a href="mailto:phenixbb-bounces@phenix-online.org" class="">mailto:phenixbb-bounces@phenix-online.org</a>]<span class="Apple-converted-space"> </span><b class="">On Behalf Of<span class="Apple-converted-space"> </span></b>Xavier Brazzolotto<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, July 24, 2018 9:50 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:phenixbb@phenix-online.org" class="">phenixbb@phenix-online.org</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[phenixbb] Ligand occupancy and conformational change<o:p class=""></o:p></span></div></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-GB" class=""><o:p class=""> </o:p></span></div><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" class="">I am struggling with a ligand bound structure.<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" 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.<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" 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.<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" class="">Hope I did myself clear.<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" class="">How to deal with this situation ? I am sure that phenix.refine can do it but how ?<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" 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<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" class="">Maybe something specific in a parameter file ?<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" class="">Thank you for your help<o:p class=""></o:p></span></div></div><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="" class="">Xavier</span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></blockquote></div><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="">Xavier Brazzolotto, PhD</div><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=""><a href="mailto:xavier.brazzolotto@chemdef.fr" class="">xavier.brazzolotto@chemdef.fr</a></div><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 style="orphans: 2; widows: 2;" class=""><div class=""><br class=""></div><div class=""><b class=""><i class="">Département de Toxicologie </i><i class="">et Risques Chimiques</i></b></div><div class=""><b class=""><i class="">Unité Neurotoxiques</i></b></div><div class=""><i class=""><b class="">Institut de Recherche Biomédicale des Armées</b></i></div><div class=""><i class=""><b class="">1 Place du Général Valérie André, BP 73</b></i></div><div class=""><i class=""><b class="">91223 Brétigny sur Orge</b></i></div><div class=""><i class=""><b class="">France</b></i></div></div><div style="orphans: 2; widows: 2;" class=""><br class=""></div><div style="orphans: 2; widows: 2;" class="">Phone<span class="Apple-tab-span" style="white-space: pre;"> </span>+33 (0) <span style="text-align: -webkit-auto;" class="">1 78 65 14 00</span></div><div style="orphans: 2; widows: 2;" class=""><span style="text-align: -webkit-auto;" class="">Alt Phone<span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="text-align: -webkit-auto;" class="">+33 (0) 4 57 42 87 19</span></div><div style="orphans: 2; widows: 2;" class="">Cell<span class="Apple-tab-span" style="white-space: pre;"> </span>+33 (0) 6 58 36 39 09</div></div><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=""><br class=""></div><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=""><i style="font-family: Calibri, sans-serif; font-size: 14px; orphans: 2; widows: 2;" class="">The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. 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