- Toggle Project Tree Clicking this button will hide or unhide the Project Tree panel.
- Show Sequences When clicking this button, a split-view will appear with a sequence list editor for each of the sequence data types in the Molecule Project (Protein, DNA, RNA).
Under "Visualization" four options exist:
- Hydrogens If not present in the imported PDB file, hydrogen atoms are assigned to the molecules based on expectations to the hybridization and connectivity of the heteroatoms. Hydrogen atoms can be shown (Show all hydrogens), hidden (Hide all hydrogens) or partially shown (Show only polar hydrogens).
- Fog "Fog" is added to give a sense of depth in the view. The strength of the fog can be adjusted or it can be disabled.
- 3D projection The view is opened up towards the viewer, with a "Perspective" 3D projection. The field of view of the perspective can be adjusted, or the perspective can be disabled by selecting an orthographic 3D projection.
- Coloring The background color can be selected from a color palette by clicking on the colored box.