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<div class="moz-cite-prefix">Hi Kendall,<br>
<br>
why don't you just define one stretch of the chain as conformer A,
and the other one as conformer B, and then request that the
occupancies of A and B add up to 1, by defining <br>
<br>
refinement {<br>
refine {<br>
occupancies {<br>
constrained_group {<br>
selection = chain A and resseq 1:10 and altloc A<br>
selection = chain A and resseq 1:10 and altloc B<br>
}<br>
}<br>
}<br>
}<br>
<br>
?<br>
<br>
If you don't do this but let the default behavior then the altloc
pairing will be done per residue and I guess you don't want this
in your case.<br>
<br>
Pavel<br>
<br>
On 8/6/12 7:52 AM, Kendall Nettles wrote:<br>
</div>
<blockquote
cite="mid:58CBFF63-C6BC-480F-AC9D-2F5965F4149F@scripps.edu"
type="cite">Hi,
<div>We have a structure with the ligand showing two overlapping
conformers. When we refine it with both conformers separately,
it is pretty clear that there are substantial differences in the
protein as a result, for about a third of the protein chain. My
question is, would it be better to try to define altloc for
those specific regions, or would it be OK to refine with two
entire alternate protein chains? There is also a second protein
chain that shows only a single binding mode for the ligand.
It's a 2.0 angstrom structure with 4000 atoms and 27,000
reflections. The yellow map goes with the green model in the
attached pic. Also, do we want to let each amino acid have its
own occupancy? or should one ligand copy and one chain all have
the same occupancy? I'm leaning towards the latter since the
differences should be directly tied to the ligand binding mode. <br>
<div>
<span class="Apple-style-span" style="border-collapse:
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0px; font-size: medium; ">Kendall Nettles</span><br>
</div>
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</blockquote>
<br>
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