Pop-up Menus of MarvinSketch

There are four pop-up menus (also called context or right-click menus) available in MarvinSketch:

Atom Pop-up Menu

Bond Pop-up Menu

Object Pop-up Menu

Edit Pop-up Menu

These popup menus do not require the corresponding atom, bond or object to be selected, however there are some additional menu elements that appear only when they are selected.

Please note that when a pop-up menu appears, it is usually the combination of these menus. For example when selecting an atom and pressing the right mouse button, a popup menu appears that contains elements of the Atom Pop-up Menu and the Edit Pop-up Menu. The elements are merged together to the displayed pop-up menu.

Atom Pop-up Menu

The Atom pop-up menu appears when you right-click on an atom on the canvas. It contains options for atom-specific activities.

Menu Item	Description
Stereo	Assigns reaction stereo labels or enhanced stereo labels to atoms. See the Enhanced stereo specification for details.
Charge	Applies a charge between [-128,128] to the atom. Marvin will let you set any of these values on any atom, highlighting the Valence Errors in red upon completion. In other words, Marvin will allow you to set a charge of -5 on hydrogen, despite the fact that this is chemically impossible.
Valence	Allows you to change the valence of any atom between [0, 8].
Radical	Sets the selected atom as a radical. You can select the type of radical - monovalent, divalent, divalent singlet, divalent triplet, trivalent, trivalent doublet, trivalent quartet. The Off option removes the radical designation.
Isotope	The Isotope submenu contains a list of the isotopes of the selected element, dynamically generated based on the selected atom. Select an isotope to set or change the isotope number or choose Off to reset the default atom type (no isotope).
Map	Set map labels/identifiers on the selected atoms that do not change while altering the molecule. They are useful when dealing with reactions, and can be saved in SMILES and MDL formats.
R-group	Change the selected atom to an R-group label. R-groups symbolize alternative substituents.
Link Node	Link node specifies rings or chains of variable size.
Attachment Point	If the selected atom is part of a group (R-group definition or abbreviated group), you can specify an attachment point.
Delete	Removes the atom from the molecule.
Add Branch	Adds a new bond with implicit hydrogen to the selected atom. This option is disabled for atoms that can have no more bonds.
Format	Change atom drawing properties.
Add To My Templates	Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.

Menu Item

Description

Stereo

Assigns reaction stereo labels or enhanced stereo labels to atoms. See the Enhanced stereo specification for details.

Charge

Applies a charge between [-128,128] to the atom. Marvin will let you set any of these values on any atom, highlighting the Valence Errors in red upon completion. In other words, Marvin will allow you to set a charge of -5 on hydrogen, despite the fact that this is chemically impossible.

Valence

Allows you to change the valence of any atom between [0, 8].

Radical

Sets the selected atom as a radical. You can select the type of radical - monovalent, divalent, divalent singlet, divalent triplet, trivalent, trivalent doublet, trivalent quartet. The Off option removes the radical designation.

Isotope

The Isotope submenu contains a list of the isotopes of the selected element, dynamically generated based on the selected atom. Select an isotope to set or change the isotope number or choose Off to reset the default atom type (no isotope).

Map

Set map labels/identifiers on the selected atoms that do not change while altering the molecule. They are useful when dealing with reactions, and can be saved in SMILES and MDL formats.

R-group

Change the selected atom to an R-group label. R-groups symbolize alternative substituents.

Link Node

Link node specifies rings or chains of variable size.

Attachment Point

If the selected atom is part of a group (R-group definition or abbreviated group), you can specify an attachment point.

Delete

Removes the atom from the molecule.

Add Branch

Adds a new bond with implicit hydrogen to the selected atom. This option is disabled for atoms that can have no more bonds.

Format

Change atom drawing properties.

Add To My Templates

Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.

Bond Pop-up Menu

The bond pop-up menu appears when you right-click on a bond within the molecule. It allows you to make a number of changes to the selected bond.

Menu Item	Submenu Items	Description
Type	Single	Changes the selected bond type to Single.
Double	Changes the selected bond type to Double.
Triple	Changes the selected bond type to Triple.
Aromatic	Changes the selected bond type to Aromatic.
Bold Single	Changes the selected bond type to Bold Single.
Query bond types	Changes the selected bond to a bond type (Single Up, Single Down, Single Up or Down, Double Cis or Trans, Double C/T or Unspec, Single or Double, Single or Aromatic, Double or Aromatic, Any) for use in a query.
Attributes	Stereo Search	Uses stereoconfiguration of specified double bond when this molecule is used as a query.
In Ring	Sets a bond property so that when the molecule is used as a query, the specified bond must be in a ring to score a hit.
In Chain	Sets a bond property so that when the molecule is used as a query, the specified bond must be in a chain to score a hit.
Reacting Center	See Reacting center bond query feature description.
Align	Vertical	Orients the bond vertically.
Horizontal	Orients the bond horizontally.
Delete	Removes the bond from the molecule.
Format	Change bond drawing properties.
Add To My Templates	Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.

Menu Item

Submenu Items

Description

Type

Single

Changes the selected bond type to Single.

Double

Changes the selected bond type to Double.

Triple

Changes the selected bond type to Triple.

Aromatic

Changes the selected bond type to Aromatic.

Bold Single

Changes the selected bond type to Bold Single.

Query bond types

Changes the selected bond to a bond type (Single Up, Single Down, Single Up or Down, Double Cis or Trans, Double C/T or Unspec, Single or Double, Single or Aromatic, Double or Aromatic, Any) for use in a query.

Attributes

Stereo Search

Uses stereoconfiguration of specified double bond when this molecule is used as a query.

In Ring

Sets a bond property so that when the molecule is used as a query, the specified bond must be in a ring to score a hit.

In Chain

Sets a bond property so that when the molecule is used as a query, the specified bond must be in a chain to score a hit.

Reacting Center

See Reacting center bond query feature description.

Align

Vertical

Orients the bond vertically.

Horizontal

Orients the bond horizontally.

Delete

Removes the bond from the molecule.

Format

Change bond drawing properties.

Add To My Templates

Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.

Object Pop-up Menu

This menu appears when the context is a graphical object like Text, Bracket, or other Graphics.

Menu Item	Description
Bring to Front	Brings the selected object in front of all others.
Send to Back	Places the selected object behind all others.
Delete	Removes the object from the canvas.
Format	Change object drawing properties.
Add To My Templates	Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.

Menu Item

Description

Bring to Front

Brings the selected object in front of all others.

Send to Back

Places the selected object behind all others.

Delete

Removes the object from the canvas.

Format

Change object drawing properties.

Add To My Templates

Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.

Edit Pop-up Menu

The Edit pop-up menu appears when you right-click on open canvas space. In case there is an atom, bond or graphic object under the cursor, the appearing pop-up menu contains the elements of the Edit Pop-up Menu merged with the pop-up menu of the selected element.
Edit pop-up menu items include:

Menu Item	Description
Add/Remove Explicit Hydrogens	Switches explicit H atoms to implicit ones and vica versa. Explicit hydrogens are displayed with atoms joining its neighbor while implicit hydrogens are displayed by atom symbols only.
Add/Remove Map Atoms	Adding atom maps is an automatic assignment of map numbers to all selected atoms of a reaction by using the automapper tool.
Add/Remove Data	Attach/Remove data like stoichiometry coefficient to the molecule.
Add/Remove Absolute Stereo (CHIRAL)	Sets/Removes chiral flag for the molecule.
Add Multi-Center	Add a multi-center attachment point representing a group of atoms.
Add Position Variation Bond	Create a variable point of attachment to represent a connection point to a group of atoms.
Edit Data	Changes a previously attached data like stoichiometry coefficient of the molecule.
Link Node	Specifies query structures containing rings or chains of variable size.
R-Logic	Allows setting additional R-group conditions such as occurrence, rest H and if-then expressions to R-groups in the R-logic dialog.
Merge Reaction Fragments	Merge the selected fragments to a reactant, product or agent.
Split Reaction Fragments	Split the previously merged reaction fragments.
Format	Change atom and bond drawing properties.
Add To My Templates	Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.

Menu Item

Description

Add/Remove Explicit Hydrogens

Switches explicit H atoms to implicit ones and vica versa. Explicit hydrogens are displayed with atoms joining its neighbor while implicit hydrogens are displayed by atom symbols only.

Add/Remove Map Atoms

Adding atom maps is an automatic assignment of map numbers to all selected atoms of a reaction by using the automapper tool.

Add/Remove Data

Attach/Remove data like stoichiometry coefficient to the molecule.

Add/Remove Absolute Stereo (CHIRAL)

Sets/Removes chiral flag for the molecule.

Add Multi-Center

Add a multi-center attachment point representing a group of atoms.

Add Position Variation Bond

Create a variable point of attachment to represent a connection point to a group of atoms.

Edit Data

Changes a previously attached data like stoichiometry coefficient of the molecule.

Link Node

Specifies query structures containing rings or chains of variable size.

R-Logic

Allows setting additional R-group conditions such as occurrence, rest H and if-then expressions to R-groups in the R-logic dialog.

Merge Reaction Fragments

Merge the selected fragments to a reactant, product or agent.

Split Reaction Fragments

Split the previously merged reaction fragments.

Format

Change atom and bond drawing properties.

Add To My Templates

Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.

Pop-up elements upon Selection

Menu Item	Description
Recent	The Recent submenu contains a list of atoms and templates previously placed on the canvas. It does not include recently used bonds. You can change the drawing object by selecting one of the items in this list.
Cut	Removes and copies the selection to the clipboard.
Copy	Copies the selection to the clipboard.
Copy as	Copies the selection to the clipboard in the specified format.
Paste	Inserts the contents of the clipboard at the location of the cursor, without replacing selection.
Select All	Selects the structure being on the canvas including all fragments and graphical objects.
Create Group	Creates an abbreviated Group from the selected substructure. See the S-groups section for more information on creating and using Groups.
Flip	Flips the structure on the canvas. The submenu allows you to choose horizontally or vertically.
Mirror	Flips the object horizontally, inverting tetrahedral stereochemistry. The submenu allows you to choose horizontally or vertically.

Menu Item

Description

Recent

The Recent submenu contains a list of atoms and templates previously placed on the canvas. It does not include recently used bonds. You can change the drawing object by selecting one of the items in this list.

Cut

Removes and copies the selection to the clipboard.

Copy

Copies the selection to the clipboard.

Copy as

Copies the selection to the clipboard in the specified format.

Paste

Inserts the contents of the clipboard at the location of the cursor, without replacing selection.

Select All

Selects the structure being on the canvas including all fragments and graphical objects.

Create Group

Creates an abbreviated Group from the selected substructure. See the S-groups section for more information on creating and using Groups.

Flip

Flips the structure on the canvas. The submenu allows you to choose horizontally or vertically.

Mirror

Flips the object horizontally, inverting tetrahedral stereochemistry. The submenu allows you to choose horizontally or vertically.