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Hi Maia,<br>
<br>
just tun off the occupancy refinement. You can do it by removing the
"*" in front of "occupancies", as illustrated below:<br>
<br>
strategy = *individual_sites rigid_body *individual_adp group_adp
*tls \<br>
*occupancies *group_anomalous<br>
<br>
Pavel.<br>
<br>
<br>
On 11/4/2008 11:26 AM, chern wrote:
<blockquote cite="mid:64A8F16D486E46C2BA961A2C4E093A41@baby" type="cite">
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<div><font face="Arial" size="2">How can I give occupancy 0.5 to my
ligands and avoid occupancy refinement? Because the refinement gave me
some atoms with occupancy 0.0 and adjacent atoms with occupancy 1.0 in
the same ligand. </font></div>
<blockquote
style="border-left: 2px solid rgb(0, 0, 0); padding-right: 0px; padding-left: 5px; margin-left: 5px; margin-right: 0px;">
<div
style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">-----
Original Message ----- </div>
<div
style="background: rgb(228, 228, 228) none repeat scroll 0%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial; font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>From:</b>
<a moz-do-not-send="true" title="PAfonine@lbl.gov"
href="mailto:PAfonine@lbl.gov">Pavel Afonine</a> </div>
<div
style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>To:</b>
<a moz-do-not-send="true" title="rwgk@cci.lbl.gov"
href="mailto:rwgk@cci.lbl.gov">Ralf W. Grosse-Kunstleve</a> ; <a
moz-do-not-send="true" title="phenixbb@phenix-online.org"
href="mailto:phenixbb@phenix-online.org">PHENIX user mailing list</a> </div>
<div
style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>Sent:</b>
Tuesday, November 04, 2008 12:15 PM</div>
<div
style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>Subject:</b>
Re: [phenixbb] refine occupancies for MET/MSE double conformations</div>
<div><br>
</div>
Ralf,<br>
<br>
it's not that uncommon. See for example:<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.rcsb.org/pdb/files/1ejg.pdb">http://www.rcsb.org/pdb/files/1ejg.pdb</a><br>
<br>
Also, you may want to couple partially occupied residue's side chain
with partially occupied water. <br>
<br>
Pavel.<br>
<br>
<br>
On 11/4/2008 9:36 AM, Ralf W. Grosse-Kunstleve wrote:
<blockquote cite="mid:200811041736.mA4Ha88v018031@cci.lbl.gov"
type="cite">
<pre wrap="">Hi Tassos,
</pre>
<blockquote type="cite">
<pre wrap="">However, I want to refine my MET residues in double conformations, one
as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy
to start with.
</pre>
</blockquote>
<pre wrap=""><!---->
In addition to what Pavel wrote: I just tried out the AMET BMSE mix
without giving any manual atom selections, and it works fine for me.
(P.S.: I'm thrilled to see this use of the
multiple-conformers-with-mixed-residue-names feature,
since it was a lot of work.)
Ralf
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<p> </p>
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