<div dir="ltr"><div><div><div>Hi Helena,<br><br></div>I believer this is the relevant bit from the manual:<br><a href="https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement">https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement</a> (in the examples)<br><br><ol class=""><li value="4"><p class="">Complex occupancy refinement strategy (combination of various available
occupancy refinement types):</p>
<pre class="">% phenix.refine data.hkl model.pdb strategy=occupancies occ.params
</pre>
</li></ol>
<p>The amount of atom selections makes it inconvenient to type them all from the
command line. This is why the parameter file <tt class="">occ.params</tt> is used and it
contains following lines:</p>
<pre class="">refinement {
refine {
occupancies {
individual = element BR or water
individual = element Zn
constrained_group {
selection = chain A and resseq 1
}
constrained_group {
selection = chain A and resseq 2
selection = chain A and resseq 3
}
constrained_group {
selection = chain X and resname MAN
selection = chain X and resseq 42
selection = chain X and resseq 121
}
remove_selection = chain B and resseq 1 and name O
remove_selection = chain B and resseq 3 and name O
}
}
}
</pre><br><br></div>Hope this helps,<br></div>Folmer<br></div><div class="gmail_extra"><br><div class="gmail_quote">2016-01-11 13:14 GMT+01:00 Christian Roth <span dir="ltr"><<a href="mailto:christianroth034@gmail.com" target="_blank">christianroth034@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Helena, <br>
Indeed you have to group the relevant aa and the respective water together in a constrained group to avoid your problem and get the occupancies add up to 1. This us described in the manual under occupancy refinement. I can't access the manual at the moment to give you a more detailed answer.</p>
<p dir="ltr">Cheers</p>
<p dir="ltr">Christian</p>
<div class="gmail_quote"><div><div class="h5">On 11 Jan 2016 11:56, "Helena Taberman" <<a href="mailto:helena.taberman@uef.fi" target="_blank">helena.taberman@uef.fi</a>> wrote:<br type="attribution"></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<div style="word-wrap:break-word">
Hi,
<div><br>
</div>
<div>I’m trying to refine a structure determined to 1.6 Å resolution. There’s several residues with additional conformations and waters with partial occupancies stating that they would be there when the conformation of the residues allows it. When
I try to refine these conformations and partially occupied waters together the refinement kicks the second conformations and water molecules out of their densities, since they are obviously too close to the other additional conformations of the residues or
the following residues. What could I do? Should I somehow group them together or what?</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Helena</div>
<div><br>
</div>
<div>
<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;word-wrap:break-word">
Helena Taberman, Ph.D.<br>
<br>
University of Eastern Finland<br>
Department of Chemistry<br>
Joensuu Campus<br>
P.O. Box 111<br>
FI-80101 Joensuu, FINLAND<br>
<br>
Mobile: <a href="tel:%2B358%2050%20337%202488" value="+358503372488" target="_blank">+358 50 337 2488</a><br>
<br>
</div>
</div>
<br>
</div>
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