<div dir="ltr">Hi John,<div><br></div><div>Why don't you make 3 alternative conformations for helix 589:598 as well? In this case you would define constrained_group with 3 selections, very much like in the example 7 you are referring to. </div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jun 6, 2018 at 11:06 AM, John Michael Bruning <span dir="ltr"><<a href="mailto:bruning@stanford.edu" target="_blank">bruning@stanford.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p style="margin-top:0;margin-bottom:0">Hi,</p>
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<p style="margin-top:0;margin-bottom:0">I have a very flexible covalent adduct that adopts three alternative conformations <span>(A,B,C)</span> in my structure . Conformations A and C are solvent exposed, while conformation B is buried. The buried conformation
B displaces a regulatory helix (resseq 589:598) by a few angstrom, while the solvent exposed conformations do not displace this helix. I can't seem to write a occupancy .params file that fulfills:</p>
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<p style="margin-top:0;margin-bottom:0">1.) occ. of ligand conformation B = occ. of displaced helix conformation # coupling of ligand binding with helix displacement</p>
<p style="margin-top:0;margin-bottom:0">2.) occ. non-displaced helix conformation = (1 - occ. displaced helix conformation)</p>
<p style="margin-top:0;margin-bottom:0">3.) sum occ. ligand conformations A+B+C = 1 # assuming protein was initially labeled 100%</p>
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<p style="margin-top:0;margin-bottom:0">It seems like #7 from <a href="http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12" rel="noopener noreferrer" id="m_-8064137865736568330LPlnk44577" class="m_-8064137865736568330x_OWAAutoLink" target="_blank">
http://www.phenix-online.org/<wbr>newsletter/CCN_2015_07.pdf#<wbr>page=12</a> is my situation, but I can't quite seem to modify this for my case. For example, something like:</p>
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<div>constrained_group {<br>
selection = chain A and resname CPE and altid B or chain A and resseq 589:598 and altid B}</div>
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<p style="margin-top:0;margin-bottom:0">Captures the concerted conformation aspect (1) (occupancy for ligand conformation B = occupancy for displaced helix) and the sum occupancy of the displaced and non-displaced helix = 1 (2), but the sum of the the alternative
conformations A+B+C > 1.0 (w/ A+C = 1.0) (3)<br>
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<p style="margin-top:0;margin-bottom:0">Incidentally, my resolution is 2.4 Ang. Thanks for any help!<br>
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<p><span style="font-family:"Courier New",monospace,serif,"EmojiFont";font-size:11pt">Cheers,
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<p><span style="font-family:"Courier New",monospace,serif,"EmojiFont""><span style="font-size:11pt"> </span><span style="font-size:11pt">J</span><span style="font-size:11pt">ohn</span></span></p>
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<p><span style="font-family:"Courier New",monospace;font-size:11pt">Cheers, </span>
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<p><span style="font-family:"Courier New",monospace"><span style="font-size:11pt"> </span><span style="font-size:11pt">J</span><span style="font-size:11pt">ohn</span></span></p>
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<span style="font-family:"Courier New",monospace;font-size:11pt">******************************<wbr>*</span>****<br>
<p><span style="font-family:"Courier New",monospace;font-size:11pt">John Bruning, Post-Doctoral Scholar</span><span style="font-family:"Courier New",monospace;font-size:11pt"></span></p>
<p><span style="font-family:"Courier New",monospace;font-size:11pt">Stanford University, Glenn Lab</span></p>
<p><span style="font-family:"Courier New",monospace;font-size:11pt">CCSR Building, #3110</span></p>
<p><span style="font-family:"Courier New",monospace;font-size:11pt">******************************<wbr>*</span>****<br>
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