Figure 7.

Refinement and validation. (a) shows the results of refinement using REFMAC5 via the CCP4i2 GUI after fitting 3-aminobenzamide into PDB entry 3kcz as demonstrated in Fig. 2 ▸. After refinement, the ligand is analysed using Coot by displaying environment distances, isolated dots and ligand distortions (b). It is evident that the ligand is in an incorrect conformation. Swapping the O and N atoms results in better stereochemistry, as is evident after re-refining the model using REFMAC5 and re-analysing the model in Coot (c). Tools such as ‘Torsion General’ are useful for such manual editing (found in the side bar to the right of the main Coot window). A two-dimensional depiction of the environment of the ligand is shown using FLEV in Coot (d).