- Hydrogens 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.
- Clipping plane This option makes it possible to add an imaginary plane at a specified distance along the camera's line of sight. Only objects behind this plane will be drawn. It is possible to clip only surfaces, or to clip surfaces together with proteins and nucleic acids. Small molecules, like ligands and water molecules, are never clipped.
- 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.
Snapshots of the molecule visualization To save the current view as a picture, right-click in the View Area and select "File" and "Export Graphics". Another way to save an image is by pressing the "Graphics" button in the Workbench toolbar (). Next, select the location where you wish to save the image, select file format (PNG, JPEG, or TIFF), and provide a name, if you wish to use another name than the default name.
You can also save the current view directly on data with a custom name, so that it can later be applied (see View settings for the Side Panel).