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<p>Hi Vatsal,<br>
</p>
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<p class="MsoNormal">I had 2 questions regarding occupancy and
maps generated in ligand-bound regions for various ligand
models potentially present in the structure:</p>
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style="margin-left:0cm;mso-list:l0 level1 lfo2">I’ve been
working with some 2.0 angstrom structures and trying out
refinements with 2 sets of bound ligands at varying
occupancies (at the same active site) to get an approximate
idea of their relative populations in the structure. For one
set of ligands, I observe 2Fo-Fc density in regions uniquely
occupied by them even when their occupancy is zero. Could
there be a reason why this is the case?</li>
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<p>how you know that their occupancy is zero? Did you try to refine
occupancy starting with some non-zero value and it refined to
zero? If the ligand is there and it is not present in your model
and you can see some evidence of it in Fo-Fc and 2Fo-Fc maps, then
the ligand is needed there! Or could it be the occupancy
refinement wasn't set up well and resulted in zero value?<br>
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style="margin-left:0cm;mso-list:l0 level1 lfo2">Additionally,
I observe red Fo-Fc density in the same region when the
occupancy is set to 1.0. It disappears at lower occupancies
of 0.7 indicating that a lower population of this ligand is
present. However, when the occupancy is very low, we don’t
see an equivalent green Fo-Fc density popping up in the same
region. Could there be a reason for why the red Fo-Fc
density at high occupancy doesn’t translate to green Fo-Fc
for the same region at low occupancy?</li>
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<p>Negative Fo-Fc map in the presence of fully occupied ligand in
the model obviously means there is more scaterring in the model
than needed. It is unsurprising that negative density disappears
when you lower the occupancy. All this tells me only one thing:
you need to *refine* occupancy.<br>
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<p class="MsoNormal">Any information or resources that could
give me more insight into this question would be really
helpful!</p>
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<p>This is relevant to your questions:</p>
<p><a class="moz-txt-link-freetext" href="https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12">https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12</a></p>
<p>Pavel</p>
<p><br>
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