| Manipulations | Mouse Actions | Key Shortcuts |
| Popup Menu | Right click | [M] |
| Rotate in 3D | Left click and Drag (hold down mouse left button while moving the pointer) | [R] |
| Zoom | [Shift] and Left click and Drag or Right click > Mouse > Zoom + Left click and drag | [Z] |
| Translate | [Ctrl] and Left click and Drag or Right click > Mouse > Translate + Left click and drag | [T] |
| Rotate in plane X^Y | [Alt] and Left click and Drag or Right click > Mouse > Rotate XY + Left click and drag | [X] |
| Menus | Options | Actions | Key Shortcuts |
| Spin | Model auto-rotation | [I] | |
| Animation | Multi-models molecular animation | [J] | |
| Display | Wireframe | Multi-bonds wireframe representation | [W] |
| Stick | Cylinder bonds representation | [S] | |
| Ball & Stick | Atoms and bonds representation | [K] | |
| Ball | Spherical atoms representation (Van der Walls radii) | [B] | |
| Backbone | Backbone alpha carbons representation for Proteins (Ca-Ca) and oxygen phosphoester for Nucleic acids (O3'-O3') | . | |
| Color | CPK Atom | CPK color coding scheme according to atom (element) type | [A] |
| Residues | Amino Acids or Nucleotides color coding scheme | . | |
| Shapely | Residues colour scheme derived from Rasmol (Bob Flettericks' "Shapely Models") | . | |
| Group | Spectral colour scheme based on residues position in protein/nucleotide sequence (blue = amino / 5' to red = carboxy / 3') |
. | |
| Chain | Chains (or models) color scheme | [C] | |
| Temperature | Spectral colour scheme based on protein anisotropic temperature (B factor) (blue = cold to red = hot') |
. | |
| User | User defined plain colour (32 supported colours, see Colour Table) . | . | |
| Options | Hydrogen | View/Mask Hydrogen | [H] |
| Labels | Atoms labeling | [L] | |
| Fastmove | Wireframe style on move | [F] | |
| Lighting | Ambient lighting (over/under expose model and background) | . | |
| Reset | Initial size and position | [O] | |
| Select | Identity | Identify pointed atom or group | [Y] |
| Distance | Interatomic distance measure | [D] | |
| Angle | Bonds angle measure | [V] | |
| Torsion | Dihedral angle measure | [N] | |
| Highlight | Highlight preselected atoms or molecule regions | [G] | |
| About | Molecule | Molecule name, number of atoms, bonds, groups | [E] |
| Chemis3D | Informations, Version and Copyright | [3] | |
| Quick Help | This help (if present in the applet's directory) | [Q] | |
| Full Help ? | Chemis3D Web Site | [?] | |
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> Chemis3D Color Table | |||