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You can also do group occupancy refinement: refine one occupancy for
the whole ligand - in this case you don't need to put an ad hoc value.
The current limitation (bug) is that the starting occupancy values in
the input PDB file for that ligand must be all 1.0.<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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</pre>
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<p> </p>
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