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 context pop-up menu,in this case the Atom Pop-up Menu, the Edit Pop-up Menu, and the Selection 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 that also can be accessed from the Atom Menu.

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	Changes the selected atom to an R-group label. R-groups symbolize alternative substituents.
R-group attachment	Adds R-group attachment point to the selected atom.
R-group attachment order	Defines the order of the R-group or deletes R-group attachment point.
Link Node	Link node specifies rings or chains of variable size.
Add S-group attachment	Creates an attachment point on the selected atom of an S-group.
Remove S-group attachment	Removes the last attachment point from the selected atom of an S-group.

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

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

R-group attachment

Adds R-group attachment point to the selected atom.

R-group attachment order

Defines the order of the R-group or deletes R-group attachment point.

Link Node

Link node specifies rings or chains of variable size.

Add S-group attachment

Creates an attachment point on the selected atom of an S-group.

Remove S-group attachment

Removes the last attachment point from the selected atom of an S-group.

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. It contains options for bond-specific activities that also can be accessed from the Bond Menu.

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.
Wedge bond types	Changes the selected bond to a Wedge bond type to represent a stereo bond: Single Up or Single Down. These bond types are active only in 2D.
Query bond types	Changes the selected bond to a bond type to be used in a query: Single Up or Down, Double Cis or Trans, Double C/T or Unspec, Single or Double, Single or Aromatic, Double or Aromatic, Any.
Coordinate	Changes the selected bond type to Coordinate.
Bold	Thickens the selected bond.
Hashed	Changes the selected bond hashed.
Topology		The following options can be set as bond property when the molecule is used as a query.
None	Removes defined bond topologies.
In Ring	The specified bond must be in a ring to score a hit.
In Chain	The specified bond must be in a chain to score a hit.
Reacting Center		The following bond property options can be set in case of drawing reaction search queries. See Reacting center bond for further query feature descriptions.
None	Removes added bond property.
Center	Specifies that the bond takes part in the reaction.
Make or Break	The assigned bond can form or disappear in the reaction.
Change	The assigned bond remains and can alter during the reaction.
Make and Change	The assigned bond can form, break,or change its type during the reaction.
Not Center	The assigned bond can not be the reaction center.
Stereo Search	Uses stereoconfiguration of specified double bond when the molecule is used as a query.
Arrange	Bring to Front	Brings the selected bond in front of the others.
Send to Back	Sends the selected bond to the back of the others.
Align	Horizontally	Orients the selected bond horizontally.
Vertically	Orients the bond vertically.

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.

Wedge bond types

Changes the selected bond to a Wedge bond type to represent a stereo bond: Single Up or Single Down.
These bond types are active only in 2D.

Query bond types

Changes the selected bond to a bond type to be used in a query:
Single Up or Down, Double Cis or Trans, Double C/T or Unspec, Single or Double, Single or Aromatic, Double or Aromatic, Any.

Coordinate

Changes the selected bond type to Coordinate.

Bold

Thickens the selected bond.

Hashed

Changes the selected bond hashed.

Topology

The following options can be set as bond property when the molecule is used as a query.

None

Removes defined bond topologies.

In Ring

The specified bond must be in a ring to score a hit.

In Chain

The specified bond must be in a chain to score a hit.

Reacting Center

The following bond property options can be set in case of drawing reaction search queries. See Reacting center bond for further query feature descriptions.

None

Removes added bond property.

Center

Specifies that the bond takes part in the reaction.

Make or Break

The assigned bond can form or disappear in the reaction.

Change

The assigned bond remains and can alter during the reaction.

Make and Change

The assigned bond can form, break,or change its type during the reaction.

Not Center

The assigned bond can not be the reaction center.

Stereo Search

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

Arrange

Bring to Front

Brings the selected bond in front of the others.

Send to Back

Sends the selected bond to the back of the others.

Align

Horizontally

Orients the selected bond horizontally.

Vertically

Orients the bond vertically.

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.

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.

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

Menu Item

Description

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.

Group

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

Pop-up elements upon Selection

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.
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.
Transformation > Drag Selection	The selected part of the molecule can be moved by dragging the mark box with your mouse or with the proper arrow keys.
Transformation > Rotate in 2D	The selection can be rotated in the plane of the canvas with changing coordinates.
Transformation > Rotate in 3D	The selected part of the molecule will be rotated according to the chosen rotation mode.
Transformation > Flip	Flips the structure on the canvas. The submenu allows you to choose horizontally or vertically.
Transformation > Mirror	Flips the object horizontally, inverting tetrahedral stereochemistry. The submenu allows you to choose horizontally or vertically.
Transformation > Invert	Reflects the selected fragment(s) through the geometric or arbitrary center.
Document Style	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.

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.

Transformation > Drag Selection

The selected part of the molecule can be moved by dragging the mark box with your mouse or with the proper arrow keys.

Transformation > Rotate in 2D

The selection can be rotated in the plane of the canvas with changing coordinates.

Transformation > Rotate in 3D

The selected part of the molecule will be rotated according to the chosen rotation mode.

Transformation > Flip

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

Transformation > Mirror

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

Transformation > Invert

Reflects the selected fragment(s) through the geometric or arbitrary center.

Document Style

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.