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Hello Masaki,<br>
<br>
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<div class="WordSection1"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"
lang="EN-US">We determined the structure of an
enzyme-substrate complex. The substrate of the enzyme contains
some partially occupied atoms. We were able to calculate the
occupancies of these atoms using PHENIX_refine.<o:p></o:p></span>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"
lang="EN-US">By the way, I would like to know the
uncertainties of the occupancies of these atoms. How can I
estimate the uncertainties? For example, the occupancy of an
atom was calculated as 0.65; can we write it as 0.65 (+/-
0.05) or 0.65 (+/- 0.1)? �I know that it is related to
B-factor and depends on the resolution (number of
diffraction data per parameters), but I would like to know
how to estimate (calculate?) the uncertainty.� Could someone
tell me about this issue?</span><br>
</p>
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</blockquote>
<br>
an approximation to what you want can be easily achieved as
following:<br>
<br>
1) create 10-100 structures where occupancies in question are
perturbed and vary from say 0.1-0.9. Also slightly perturb B-factors
of atoms that surround these atoms.<br>
<br>
2) Refine all these perturbed structures using refinement protocols
that you usually use (the one used to obtain your final structure).
Make sure to use sufficient amount of refinement macro-cycles so
that refinement achieves near-convergence.<br>
<br>
3) Extract occupancies in question. They will make some distribution
and the spread of that distribution will tell you hint you the
uncertainty.<br>
<br>
Pavel� <br>
<br>
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