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 > Wireframe with Knobs

Displays bonds as thin lines, Carbon atoms as knobs, and other atoms 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.