The 2D depiction panel

Image ligand_optimizer_2d_panel
Figure 9.31: The 2D depiction panel, shown together with the issue list panel. The two green dots on the 2D depictions indicates the selection of a covalent bond.

The 2D depiction panel shows the molecule currently being optimized (figure 9.31). It is possible to select atoms from either the 2D or the 3D view. A bond can be selected by selecting the two atoms it connects.

A checkbox makes it possible to toggle hydrogens on and off, which can be useful when specifying the attachment point when adding new fragments. It is possible to zoom in and out on the 2D depiction using the mouse wheel, making it easy to navigate larger ligands.