Mouse Mode > Sketch

The Sketch mode allows drawing into the canvas.

Mouse Mode > Zoom

Zoom the content of the canvas by dragging the mouse without modifying atom coordinates.

Mouse Mode > 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.

Mouse Mode > Reset View

Restores the starting view as modified by rotation and zoom.

Zoom Level

Allows you to select a magnification percentage from the list or to type a custom percentage.

Structure 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.

Structure Display > Wireframe

Displays bonds as thin lines, and atoms (except Carbon) as symbols.

Structure Display > Wireframe with Knobs

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

Structure Display > Stick

Displays bonds as thick lines, and atoms (except Carbon) as symbols.

Structure Display > Ball and Stick

Displays bonds as thick lines, atoms as shaded balls, and atoms (except Carbon and Hydrogen) as symbols on balls.

Structure 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 with different colors the new Peptide Bridge bonds which are crosslinking the peptide chains.

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 possible

Always show atom chirality (R/S) including not defined stereocenters (?) .

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 Display > 1-letter

View peptide sequence with 1-letter aminoacid codes.

Peptide Display > 3-letter

View peptide sequence with 3-letter aminoacid 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 > Graph Invariants

Toggles the display of graph invariants (canonical 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.

Advanced > S-group Attachment

Toggles the display of the attachement points. Default setting is On.

Pages > Fit Page Width

Adjusts the width of the current page to the width of the canvas.

Pages > Fit Page Height

Adjusts the height of the current page to the height of the canvas.

Pages > Fit Page

Adjusts the current page so that the whole current page will be placed centralized within the canvas.

Pages > Previous Page

Goes to the previous page of multipage molecular document.

Pages > Next Page

Goes to the next page of multipage molecular document.

Pages > First Page

Goes to the first page of multipage molecular document.

Pages > Last Page

Goes to the last page of multipage molecular document.

Pages > Goto Page

Goes directly to a specific page by entering a number in the appearing dialog window.

Open MarvinSpace

Launches a MarvinSpace window containing the current molecule from the Sketcher.

Toolbars > Toolbars

Sets the visibility of individual toolbars.

Menubar

Sets the visibility of the main menubar.

Status Bar

Sets the visibility of the status bar.

Grid

Toggles the display of the grid.

Guideline

Toggles the display of the moveable guidelines.

Editor Style > Configurations

Lists the available configurations, and allows quick switch.

Editor Style > Configuration Settings

Configurations are GUI alternatives storing whole menu, toolbar and popup personalizations. This makes easy to define and quickly change the GUI for various purposes like sketching, publishing, teaching, etc.

Editor Style > Reset Current Configuration

Removes all local modifications made on the active GUI configuration. Note that this action cannot be undone.

Editor Style > Customize

Customization allows you to personalize the GUI of MarvinSketch including menus, toolbars and keyboard shortcuts.