<div dir="ltr">Hi Xavier,<div><br></div><div>In addition to Edward's suggestion, you can have a look at "13 typical occupancy refinement scenarios and available options in phenix.refine" article here:</div><div><a href="http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12">http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12</a><br></div><div><br></div><div>Scenario #7 looks like your case, but you will have your ligand only in one conformation.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jul 24, 2018 at 8:25 AM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu" target="_blank">BerryE@upstate.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">You can make very general alternate conformations with the "constrained_group" construction.<br>
Say the loop is N12:14 and ligand is R221 present only in A conformation. You can also add waters<br>
to either conformation. The following is for running from .eff script, but I expect it is available from the Gui. There is a detailed description of handling alt conf in one of the newsletters.<br>
<br>
refine {<br>
occupancies {<br>
constrained_group {<br>
selection = ((chain N and resseq 12:14) or (chain R and resid 221)) \<br>
and altloc A<br>
selection = (chain N and resseq 12:14) and altloc B<div><div class="h5"><br>
}<br>
<br>
}}<br>
On 07/24/2018 02:49 AM, Xavier Brazzolotto wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<br>
I am struggling with a ligand bound structure.<br>
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.<br>
<br>
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.<br>
Hope I did myself clear.<br>
<br>
How to deal with this situation ? I am sure that phenix.refine can do it but how ?<br>
What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X<br>
Maybe something specific in a parameter file ?<br>
<br>
Thank you for your help<br>
Xavier<br>
<br>
<br></div></div>
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