| Transform > Translate or Drag |
Shifts the structure on the canvas with the mouse. |
| Transform > Zoom |
Zoom the content of the canvas by dragging the mouse without modifying atom coordinates. |
| Transform > Rotate in 3D |
Spin the structure around its central point in 3 dimension with the help of the mouse without modifying atom coordinates. Compare it to the Free 3D rotation of Edit Menu, which affects the molecular coordinates. |
| Transform > Rotate in 2D |
Spin the structure around its central point in 2 dimension with the help of the mouse without modifying atom coordinates. |
| Transform>Zoom/Rotate |
Uses the zoom transformation when the mouse is moved vertically and uses rotation when the mouse is moved horizontally. |
| Transform > Reset View |
Restores the starting view as modified by rotation and zoom. |
| Animation>Play/Pause |
Starts/stops an XYZ animation sequence, or starts rotating the selected molecule in 3D. |
| Animation>Rewind |
Stops the animation and resets it to the starting position. |
| Animation>Quantize Spin |
Changes the number of rotations from the current value to the closest integer, for example 1.8 rotation / 198 frames is changed to 2 rotations / 198 frames. The effect is irreversible. |
| Animation>Drag to Spin |
Allows changing the direction and speed of the rotation using mouse dragging. |
| Display > Atom Symbols in 3D |
Sets atom symbol visibility in 3D mode. Note that in 3D mode, atoms may become invisible in Wireframe and Stick mode by hiding atom symbols. |
| Display > Wireframe |
Displays bonds as thin lines, and atoms (except Carbon) as symbols. |
| Display > Stick |
Displays bonds as thick lines, and atoms (except Carbon) as symbols. |
| Display > Ball and Stick |
Displays bonds as thick lines, atoms as shaded balls, and atoms (except Carbon and Hydrogen) as symbols on balls. |
| Display > Spacefill |
Displays atoms as large shaded balls, and atoms (except Carbon and Hydrogen) as symbols on the balls. |
| Colors > Monochrome |
Displays all atoms with default drawing color. |
| Colors > CPK |
Displays all atoms with Corey-Pauling-Kultun colors. |
| Colors > Shapely |
This color scheme is based on RasMol's shapely color scheme for nucleic and amino acids. |
| Colors > Group |
Coloring atoms based on PDB residue numbers. |
| Colors > Atom/Bond Sets |
Colors atoms and bonds according to the color of the pre-defined set they belong to. |
| Colors > Peptide Bridges |
Colors bridges in peptide/proteins. |
| Colors > Background |
Sets custom background color with adjusted default drawing color. |
| Colors > White Background |
Sets the background color to white and the default drawing color to black. |
| Colors > Black Background |
Sets the background color to black and the default drawing color to white. |
| Stereo > R/S Labels > All |
Always show atom chirality (R/S). |
| Stereo > R/S Labels > Absolute Stereo |
Show atom chirality if chiral flag is set for the molecule or the atom's enhanced stereo type is absolute. |
| Stereo > R/S Labels > None |
Do not show atom chirality (R/S). |
| Stereo > E/Z Labels |
Toggles the display of absolute double bond stereo configuration labels. Bonds known to have an (E) or (Z) configuration will be marked as such. |
| Stereo > M/P Labels |
Toggles the display of axial stereochemistry labels M and P |
| Stereo > Absolute Labels |
Toggles the display of the Absolute label if the chiral flag is set on the molecule. |
| Implicit Hydrogens > On All |
View hydrogens by symbol on all atoms. This option is disabled in Spacefill and Ball & Stick display modes. |
| Implicit Hydrogens > On Hetero and Terminal |
View hydrogens by symbol on hetero and terminal carbon atoms. This option is disabled in Spacefill and Ball & Stick display modes. |
| Implicit Hydrogens > On Hetero |
View hydrogens by symbol on hetero atoms only. This option is disabled in Spacefill and Ball & Stick display modes. |
| Implicit Hydrogens > Off |
Disable hydrogens by symbol on all atoms. |
| Peptide Sequence > 1-letter |
View peptides as their 1-letter codes. |
| Peptide Sequence > 3-letter |
View peptides as their 3-letter codes. |
| Advanced > Atom Numbering > Off |
Disable the visibility of atom indices. |
| Advanced > Atom Numbering > Atom Number |
Enable the visibility of unique internal atom indices. The indices are continuous starting from 1. |
| Advanced > Atom Numbering > IUPAC Numbering |
Enable the visibility of IUPAC numbering of atoms in a molecule. It is synchronized with the numbering of "Structure to name" option. |
| Advanced > Atom Properties |
Toggles the visibility of atom properties. |
| Advanced > Atom Mapping |
Toggles the visibility of atom mapping labels. |
| Advanced > Bond Lengths |
Toggles the display of bond lengths in Angstroms on the middle of the bonds. |
| Advanced > Lone Pairs |
Toggles the display of lone pairs. |
| Advanced > R-groups |
Toggles the display of R-group definitions. |
| Advanced > R-logic |
Toggles the display of R-logic definitions. |
| Advanced > Valence |
Toggles the display of valence numbers. Default setting is On. |
| Advanced > Ligand Error |
Toggles the display of ligand errors. Default setting is On. |
| Rescale cells > Separately |
Changes the zoom of each cells individually so that molecules best fit their own cell. |
| Rescale cells > Uniformly |
Changes the zoom ratio of all cells to the same value with which all molecules are fully visible in their own cell. |
| Open MarvinSpace |
Launches a MarvinSpace window containing the current molecule. |