<div dir="ltr">Hi Helena,<div><br></div><div>My best guess is that either your selections or altloc in .pdb file are wrong.</div><div><br></div><div>We are glad to help you with this issue! To get the precise answer to your question we need your model and data files (.pdb and .mtz files, and .cif files for ligand if any). Please send them to me directly (off-list) and indicate the residues (atoms) in question. </div><div><br></div><div>Your data will be kept in confidence.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jan 13, 2016 at 11:59 PM, Helena Taberman <span dir="ltr"><<a href="mailto:helena.taberman@uef.fi" target="_blank">helena.taberman@uef.fi</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<br>
<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">
Hi,</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">
<br>
</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">
Thanks for your advice. It’s still not working. I use the phenix gui version and if I set, for example,<br>
<br>
</div>
<div style="text-align:start;text-indent:0px;word-wrap:break-word">
chain A and resid 249</div>
<div style="text-align:start;text-indent:0px;word-wrap:break-word">
chain A and resid 252</div>
<div style="text-align:start;text-indent:0px;word-wrap:break-word">
chain S and resid 1702</div>
<div style="text-align:start;text-indent:0px;word-wrap:break-word">
<br>
</div>
<div style="text-align:start;text-indent:0px;word-wrap:break-word">
as a constrained group at the occupancy refinement selections (the two residues have 2 conformations both and the water is there just if the conformation of residue 252 is B) the refinement just makes the residues a constrained group alone making even their
main chain occ. something like 0.49 as for the both of the side chains too. And it also kicks them a bit out of their densities. So how to continue? What am I doing wrong?</div>
<div style="text-align:start;text-indent:0px;word-wrap:break-word">
<br>
</div>
<div style="text-align:start;text-indent:0px;word-wrap:break-word">
Best regards,</div>
<div style="text-align:start;text-indent:0px;word-wrap:break-word">
Helena</div>
</div><div><div class="h5">
<br>
<div>
<blockquote type="cite">
<div>Folmer Fredslund <<a href="mailto:folmerf@gmail.com" target="_blank">folmerf@gmail.com</a>> kirjoitti 11.1.2016 kello 15.20:</div>
<br>
<div>
<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" target="_blank">https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement</a> (in the examples)<br>
<br>
<ol>
<li value="4">
<p>Complex occupancy refinement strategy (combination of various available occupancy refinement types):</p>
<pre>% 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>occ.params</tt> is used and it contains following lines:</p>
<pre>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>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>
<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="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>
<br>
</div>
</div>
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<br>
<br clear="all">
<br>
-- <br>
<div>Folmer Fredslund<br>
</div>
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</div>
</blockquote>
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