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Hi Anna,<br>
<br>
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<span lang="EN-US"><font face="Calibri">I�m working on the
refinement of a protein mutated with an unnatural amino acid
that contains one bromine atom. This particular amino acid
is present as two rotamers. I�ve managed to introduce and do
refinements with these two unnatural, brominated rotamers in
Phenix, but the problem is that when shooting the protein
with X-rays about 30-40% of the bromine atoms get knocked
off. This means that the sum of the occupancies for the
bromine atoms of the rotamers needs to be less than 1.00.
However, the total occupancy of all the other rotamer atom
pairs must be 1.00. Is there a way in Phenix to refine
rotamers of brominated, unnatural amino acids, and at the
same time have the total occupancy less than 1.00 for the Br
atoms only? Any advice how to solve this is welcome.</font></span></div>
</blockquote>
<br>
the answer is in this newsletter article:<br>
<br>
13 typical occupancy refinement scenarios and available options in
phenix.refine<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/newsletter/">https://www.phenix-online.org/newsletter/</a><br>
<br>
Basically, all you need to do is to define each residue side chain
conformer as one constrained group consisting just that one
conformer. This will override the default behavior which groups
occupancies and make them to add up to 1. One way of doing this is
to compose a parameter file that looks like this, occ_params.eff:<br>
<br>
refinement {<br>
� refine {<br>
��� occupancies {<br>
����� constrained_group {<br>
������� selection = chain A and resseq 123 and altloc A<br>
����� }<br>
����� constrained_group {<br>
������� selection = chain A and resseq 123 and altloc B<br>
����� }<br>
��� }<br>
� }<br>
}<br>
<br>
and load it into the GUI along with all other files (PDB,
reflections, etc). This will refine one occupancy for "chain A and
resseq 123 and altloc A" and one occupancy for "chain A and resseq
123 and altloc B", and they will not be related to each other. Each
of the two occupancies will be free to refine to any value between 0
and 1.<br>
<br>
Alternatively (instead of using parameter file), you can use Atom
Selection Editor: Refinement Settings -> Select Atoms ->
Refinement Strategy -> Group Occupancies -> Add Group.<br>
<br>
Let me know if you have any questions or problems!<br>
<br>
Pavel<br>
<br>
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