journal menu
![[Figure 2]](ba5265fig2mag.jpg)
|
|
Figure 2
Automatic ligand fitting in CCP4. The SMILES string corresponding to 3-aminobenzamide is pasted into the `Make Ligand' task interface in CCP4i2 (a). Upon running the job, AceDRG is used to generate ligand restraints and RDKit is used to generate an initial conformer and a two-dimensional representation of the ligand (b). The `Manual Model Building' task is then executed to open Coot. (c) displays the model (sticks) and 2mFo − DFc density map (blue) corresponding to a structure solved with data extending to 2 Å resolution (PDB entry 3kcz; Karlberg et al., 2010  ) after manually removing the ligands. The maps are shown using Coot's default contour levels. Automatic ligand fitting is performed, using 3-aminobenzamide as the target. The focal region corresponds to the top-ranked blob identified in the masked map (orange). The ligand coordinates are nominally positioned onto the centre of the blob (d). The ligand is then optimally oriented and rigid-body refined into the masked density (e). In this case, manual intervention would be required in order to ensure favourable hydrogen bonds are satisfied: this issue is further addressed in §6 and Fig. 7. Multiple blobs are found in the map and ligands are fitted into them; the third-highest ranked ligand is automatically fitted into a blob that actually corresponds to a glycerol molecule (f). |
![[Figure 2]](ba5265fig2.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
Open 
access
access
