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![[Figure 2]](ic5118fig2mag.jpg)
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Figure 2
Examples of validation components in VA pages for EMDB entries (see text for details). The examples are for EMDB entry EMD-11145, which is a SARS-CoV-2 spike protein (Toelzer et al., 2020  ). (a) Orthogonal standard-deviation projection (shown with false colour) along the X axis. The lowest values are mapped to solid green, which may help to identify if and how masking was applied. (b) Orthogonal surface view of the raw map (calculated by averaging the two half-maps) along the X axis. (c) Overlay of the primary map (yellow, semi-transparent) and fitted model (blue) viewed along the X axis. (d) Overlay of the primary map (yellow, semi-transparent) with a mask (blue) viewed along the X axis. (e) FSC plot combining the author-provided curve (cyan) and that calculated from the two half-maps (orange) as well as various criteria used by the community to estimate resolution. The red vertical line indicates the resolution reported by the author. (f) Map–model FSC plot. FSC values are calculated between the primary map and a map calculated from the model using REFMAC (Murshudov et al., 2011). (g) Overview of map/model-fit analysis using the Q-score (Pintilie et al., 2020) both on a per-residue basis (3D view and lower part of the plot) and averaged per chain (coloured blocks at the top). The overall average score is shown in the legend (0.732 in this case). Colour ramping is used, with cyan indicating higher Q-scores (better fit). (h) RAPS plot of the primary (cyan) and raw (orange) maps. The red vertical line indicates the author-provided resolution of the map. (i) Overview of map–model fit analysis using 3D-Strudel (Istrate et al., 2021). Each row of the plot shows the 3D-Strudel score for up to 100 residues. Red dots indicate residues where the map motif of a different amino-acid type to that in the model is most similar to the local map. |
![[Figure 2]](ic5118fig2.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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