A set of measures of map quality were applied to experimental maps (or structure-factor amplitudes, phases and weights) obtained from real but re-enacted structure determinations. Each of the structures considered had been determined previously, so that phases from a refined model could be used with measured amplitudes to calculate a model map to use as a standard. The ‘true’ quality of each map was taken to be the correlation with the corresponding standard map calculated at the same nominal resolution. Each measure of quality was applied to each map and the resulting scores were saved along with the corresponding ‘true’ quality. The structure-solution process was automatically carried out by the PHENIX AutoSol wizard and each experimentally phased map that was obtained during the structure-solution process was examined in this way. To reduce the number of near-duplicate solutions considered, all solutions for a structure that had nearly identical values of the map correlation to the standard map (within a range of ±0.0005 in map correlation) were considered to be the same and only the first was used in the analysis. For comparisons involving two possible enantiomers of a solution, the two enantiomers of a solution sometimes differed only slightly (i.e. the heavy-atom substructure was nearly centrosymmetric). In these analyses of enantiomeric pairs, only those that differed by an r.m.s.d. of at least 0.5 Å were considered.
For analysis of map quality, electron-density maps and structure factors were calculated using a high-resolution limit of 2.5 Å (if data were available to that resolution), as described above for the PHENIX AutoSol wizard. Before applying each of the measures of map quality, the experimental maps were normalized to a mean of zero and a variance of unity. They were then adjusted in two steps to reduce the contribution from high density at the coordinates of heavy-atom sites. (The high density at heavy-atom sites might otherwise lead to high values for the skewness, NCS correlation, contrast and possibly other measures.) Firstly, the electron density within a radius (r) of each heavy-atom site used in phasing (where r was given by twice the resolution of the data or 5 Å, whichever was greater) was limited to values less than or equal to twice the r.m.s. (2σ) of the map. Secondly, the electron density everywhere in the map was limited to values in the range −5σ to +5σ. This modified map is referred to below as the normalized truncated experimental electron-density map.
Weighted electron-density maps were calculated in the PHENIX environment (Adams et al., 2002 ▶ ) using RESOLVE (Terwilliger, 2000 ▶ ) on a grid with a spacing of 1/3 of the high-resolution limit of the data or finer. Map correlations were obtained by calculating the correlation coefficient of a pair of maps at all the grid points in the asymmetric unit of the unit cell. Model–map correlations were calculated in the same way, except that one map was calculated from the model and an overall B factor (b_overall) was adjusted to maximize the correlation. This correlation was further maximized by adjusting a parameter (rFFT) representing the radius around atoms in the model to be included in FFT-based density calculations (typically about equal to the high-resolution limit of the data). For protein chains, an increment in isotropic thermal factors (beta_b) for each bond between side-chain atoms and the Cβ atom was also applied to maximize the correlation.
For analysis of map quality, electron-density maps and structure factors were calculated using a high-resolution limit of 2.5 Å (if data were available to that resolution), as described above for the PHENIX AutoSol wizard. Before applying each of the measures of map quality, the experimental maps were normalized to a mean of zero and a variance of unity. They were then adjusted in two steps to reduce the contribution from high density at the coordinates of heavy-atom sites. (The high density at heavy-atom sites might otherwise lead to high values for the skewness, NCS correlation, contrast and possibly other measures.) Firstly, the electron density within a radius (r) of each heavy-atom site used in phasing (where r was given by twice the resolution of the data or 5 Å, whichever was greater) was limited to values less than or equal to twice the r.m.s. (2σ) of the map. Secondly, the electron density everywhere in the map was limited to values in the range −5σ to +5σ. This modified map is referred to below as the normalized truncated experimental electron-density map.
Weighted electron-density maps were calculated in the PHENIX environment (Adams et al., 2002 ▶ ) using RESOLVE (Terwilliger, 2000 ▶ ) on a grid with a spacing of 1/3 of the high-resolution limit of the data or finer. Map correlations were obtained by calculating the correlation coefficient of a pair of maps at all the grid points in the asymmetric unit of the unit cell. Model–map correlations were calculated in the same way, except that one map was calculated from the model and an overall B factor (b_overall) was adjusted to maximize the correlation. This correlation was further maximized by adjusting a parameter (rFFT) representing the radius around atoms in the model to be included in FFT-based density calculations (typically about equal to the high-resolution limit of the data). For protein chains, an increment in isotropic thermal factors (beta_b) for each bond between side-chain atoms and the Cβ atom was also applied to maximize the correlation.
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