View Menu in MarvinSketch

This menu allows you to alter the way the molecule is displayed without modifying the structure file itself. You can change the molecule display type, background color, color scheme, error highlighting, and so on.

The View menu also contains operations to change the graphical user interface.

See also: Structure Display Options

Menu item

Icon

Description

Mouse Mode > Sketch

images/download/attachments/1805239/sketch-mode16.png

The sketch mode allows drawing into the canvas.

Mouse Mode > Zoom

images/download/thumbnails/1805239/zoom-mode24.png

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

Mouse Mode > Reset View

images/download/thumbnails/1805239/resetview24.png

Restores the starting view.

Zoom Level

N/A

You can select the magnification percentage from the list.

Structure Display > Atom Symbols in 3D

N/A

Use this menu item to switch between hiding and showing atom symbols in 3D. Note that atoms become invisible in Wireframe and Stick modes when atoms are hidden in 3D.

Structure Display > Wireframe

N/A

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

Structure Display > Stick

N/A

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

Structure Display > Ball and Stick

N/A

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

Structure Display > Spacefill

N/A

Displays atoms as large shaded balls with symbols on the balls (except Carbon and Hydrogen).

Colors > Monochrome

N/A

Displays all atoms with default drawing color.

Colors > CPK

N/A

Displays all atoms with Corey-Pauling-Kultun colors.

Colors > Shapely

N/A

This color scheme is based on RasMol's shapely color scheme for nucleic and amino acids.

Colors > Group

N/A

Colors atoms based on PDB residue numbers.

Colors > Atom/Bond Sets

N/A

Colors atoms and bonds according to the color of the pre-defined set they belong to.

Colors > Peptide Bridges

N/A

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

Colors > Background

N/A

Sets custom background color with adjusted default drawing color.

Colors > White Background

N/A

Sets the background color to white and the default drawing color to black.

Colors > Black Background

N/A

Sets the background color to black and the default drawing color to white.

Stereo > R/S Labels > All possible

N/A

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

Stereo > R/S Labels > All

N/A

Always show atom chirality (R/S).

Stereo > R/S Labels > Absolute Stereo

N/A

Show atom chirality if the chiral flag is set for the molecule or the enhanced stereo type of the atom is absolute.

Stereo > R/S Labels > None

N/A

Do not show atom chirality (R/S).

Stereo > E/Z Labels

N/A

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

N/A

Toggles the display of axial stereochemistry labels (M) and (P).

Stereo > Absolute Labels

N/A

Toggles the display of the Absolute label if the chiral flag is set on the molecule.

Implicit Hydrogens > On All

N/A

View hydrogens by symbol on all atoms. This option is disabled in Spacefill and Ball and Stick display modes.

Implicit Hydrogens > On Hetero and Terminal

N/A

View hydrogens by symbol on hetero and terminal carbon atoms. This option is disabled in Spacefill and Ball and Stick display modes.

Implicit Hydrogens > On Hetero

N/A

View hydrogens by symbol on hetero atoms only. This option is disabled in Spacefill and Ball and Stick display modes.

Implicit Hydrogens > Off

N/A

Disable hydrogens by symbol on all atoms.

Peptide Display > 1-letter

N/A

View peptide sequence with 1-letter amino acid codes.

Peptide Display > 3-letter

N/A

View peptide sequence with 3-letter amino acid codes.

Advanced > Atom Numbering > Off

N/A

Disable the visibility of atom indices.

Advanced > Atom Numbering > Atom Number

N/A

Enable the visibility of unique internal atom indices. The indices are continuous starting from 1.

Advanced > Atom Numbering > IUPAC Numbering

N/A

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

N/A

Toggles the visibility of atom properties.

Advanced > Atom Mapping

N/A

Toggles the visibility of atom mapping labels.

Advanced > Bond Lengths

N/A

Toggles the display of bond lengths in Angstroms in the middle of the bonds.

Advanced > Lone Pairs

N/A

Toggles the display of lone pairs.

Advanced > R-groups

N/A

Toggles the display of R-group definitions.

Advanced > R-logic

N/A

Toggles the display of R-logic definitions.

Advanced > Valence

N/A

Toggles the display of valence numbers. The default setting is On.

Advanced > Ligand Error

N/A

Toggles the display of ligand errors. The default setting is On.

Advanced > S-group Attachment

N/A

Toggles the display of the attachment points. The default setting is On.

Pages > Fit Page Width

images/download/thumbnails/1805239/fit-width24.png

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

Pages > Fit Page Height

images/download/thumbnails/1805239/fit-height24.png

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

Pages > Fit Page

images/download/thumbnails/1805239/fit-page24.png

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

Pages > Previous Page

images/download/thumbnails/1805239/previous24.png

Goes to the previous page of a multipage molecular document.

Pages > Next Page

images/download/thumbnails/1805239/next24.png

Goes to the next page of a multipage molecular document.

Pages > First Page

images/download/thumbnails/1805239/first24.png

Goes to the first page of a multipage molecular document.

Pages > Last Page

images/download/thumbnails/1805239/last24.png

Goes to the last page of a multipage molecular document.

Pages > Goto Page

N/A

Goes directly to a specified page.

Toolbars > Toolbars

N/A

You can toggle the visibility of the following toolbars:

  • General

  • Chemical

  • 3D editing

  • Simple Templates

  • Advanced Templates

  • Markush

  • Tools

  • Atoms

Menubar

N/A

Toggles the visibility of the main menubar.

Status Bar

N/A

Toggles the visibility of the status bar.

Grid

N/A

Toggles the visibility of the grid.

Guideline

N/A

Toggles the visibility of the moveable guidelines.

Editor Style

N/A

Lists the available configurations, and allows quick switch.

Editor Style > Configuration Settings

N/A

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

Editor Style > Reset Current Configuration

N/A

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

Editor Style > Customize

N/A

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