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. Pavel