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Figure 6
The new ligand validation in Coot in action. Shown here is the ligand CQ8 from PDB entry 4zzn. The ligand model corresponds well to the density map (shown in both panels) and (from the top panel) the bond and angles of the ligand model correspond well to expected values [the Z-values for each bond and angle are displayed on a sliding scale, with green corresponding to the most likely values (Z-values of 1 or less) and red corresponding to Z-values of 5 or greater]. The hint of red that one can see at the bottom right comes from the underlying molecule representation of ketone double-bonded oxygen. The lower panel illustrates that the manner of interaction of the ligand with the protein environment is via hydrogen bonds of typical length and that there are no bad contacts between the ligand and the protein. The colour scheme of the dots is as follows: hydrogen bonds are olive-green dots, wide contacts are purple, close contacts are light green, small overlaps are orange and bad contacts (not appropriate for this ligand model) would be red.

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ISSN: 2059-7983
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