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

Pavel Afonine pafonine at lbl.gov
Wed Feb 11 10:21:47 PST 2015

Hello Masaki,

> 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?

an approximation to what you want can be easily achieved as following:

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.

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.

3) Extract occupancies in question. They will make some distribution and 
the spread of that distribution will tell you hint you the uncertainty.


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