[phenixbb] How should we estimate the "uncertainty" of the occupancy of an atom?

Masaki UNNO unno19 at mx.ibaraki.ac.jp
Wed Feb 11 00:36:29 PST 2015



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.

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?


Best regards



Masaki UNNO

Graduate School of Science and Engineering

Ibaraki University, JAPAN

4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan

Tel&Fax +81-294-38-5041



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