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Figure 1
An outlier legend, showing each symbol used in a MolProbity multi-criterion kinemage and illustrating the relationship of the three types of all-atom contact to the atomic van der Waals (vdW) surfaces (spheres of small gray dots). The symbols for favorable hydrogen bonds and vdW contacts are included for completeness, as well as the hot-pink spikes of a clash outlier. A Cβ deviation of ≥0.25 Å is shown as a magenta ball centered on the ideal Cβ position and tangent to the modeled position. Bad rotamers are shown as gold side chains and Ramachandran outliers as heavy green lines to the midpoints of the two peptides. Bond-angle outliers are indicated by a fan of lines from the ideal to the modeled bond (red if wide, blue if narrow). Bond-length outliers are indicated as stretched (red) or compressed (blue) springs. A suspicious ribose pucker is diagnosed by the perpendicular distance from the 3′ (following) phosphate to the line of the glycosidic C1′—N1/9 bond and is flagged by a representation of that construction (in magenta if too short, as here, and in purple if too long).

Journal logoBIOLOGICAL
ISSN: 1399-0047
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