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Hi,<br>
<br>
occupancy refinement in phenix.refine does not use information about
special positions. So if it sees an atom (or groups of atoms) having
partial occupancy it will refine them to be any number between 0 and
1. This is in my to-do list to fix one day.<br>
<br>
Currently, you need to turn off the occupancy refinement for these
atoms manually using "occupancies.remove_selection".<br>
<br>
However, if the input occupancy is set to 1 then internally
phenix.refine will do the right thing with respect to special
position (it will apply the multiplicity factor), and it will not
refine it. The downside of doing it this way is that this is not
what PDB expects.<br>
<br>
Pavel.<br>
<br>
<br>
On 4/30/11 10:07 PM, Ralf W. Grosse-Kunstleve wrote:
<blockquote cite="mid:152136.43096.qm@web111407.mail.gq1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: Courier
New,courier,monaco,monospace,sans-serif; font-size: 10pt;">
<div><span>This should work as you expect in more recent phenix
versions. My recommendation is to install 1.7.1 and then try
again. -- phenix versions can co-exist. Just make sure you
source the phenix_env of the version you want to use.</span></div>
<div><span>Ralf<br>
</span></div>
<div><br>
<blockquote style="border-left: 2px solid rgb(16, 16, 255);
margin-left: 5px; padding-left: 5px;">
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<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;"><font face="Arial"
size="2">
<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
J. Fleming <a class="moz-txt-link-rfc2396E" href="mailto:moloch525@gmail.com"><moloch525@gmail.com></a><br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b><span style="font-weight: bold;">Sent:</span></b>
Saturday, April 30, 2011 9:13 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [phenixbb] Sulfate ion on 2-fold axis<br>
</font><br>
<div id="yiv695713228">Hi all,<br>
<br>
I have a sulfate ion sitting on a 2-fold axis of
symmetry. If I set all the atom occupancies to 0.5
and refine using phenix.refine (Phenix v. 1.5-2) the
occupancies are changed to 0.00 for the sulfur, 1.00
for three of the oxygen's, and 0.72 for the fourth
oxygen. Can anyone explain this?<br>
<br>
Thanks in advance,<br>
Jon<br>
</div>
</div>
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</blockquote>
</div>
</div>
</blockquote>
<br>
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