Calculation of atomic positional probability

All atoms comprising the ensemble are assigned a probability (P_i) based on the positional likelihood of atom i in a given model relative to the complete ensemble of models. F_calc electron-density maps are calculated for each model in the ensemble and 〈F_calc〉 electron-density map is calculated for the complete ensemble as (10). P_i is calculated as (12).

Calculating from an electron-density function allows for non-Gaussian distributions unlike RMSF, which is calculated from mean atomic position. These probabilities aid the visual inspection of the ensemble models and allow the observer to control the level of detail displayed (Figure 14).

Interpretation of global and local details of 1UOY ensemble model is aided by relative atomic probability (as described in ‘Materials and methods’). Ensemble models, left and centre, are colour by individual atom probability (0–1) from red to blue. Single structures, right, are coloured by individual atomic B-factor as refined in phenix.refine. (A) Global structure, selecting different probability ranges highlights partially ordered water positions. (B) Atomic probabilities of loop regain features correlate with B-factors in single structure. Anharmonic motion of Ser5 can be observed as well as anisotropic motion at Tyr7, which is shown in more detail in (C).

DOI: http://dx.doi.org/10.7554/eLife.00311.027