Visualization settings
Under "Visualization" five options exist:- 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.