Chemical Features of MarvinSketch

Table of Contents

Valence Check

MarvinSketch does not automatically correct valence errors. Instead, they are highlighted by a red underline and you may make the appropriate corrections. This option can be turned on or off using the Edit > Preferences box.


In MarvinSketch, the charge of an atom is initially set to be neutral. As bonds are added or removed, MarvinSketch adjusts the number of implicit hydrogens to let the charge remain neutral. You may change the charge of any atom using the Atom Pop-up Menu. The number of implicit hydrogens will be adjusted, if possible, to accommodate the new charge. MarvinSketch will then perform a valence check and highlight the atom if an error is found.


MarvinSketch allows you to draw reactions in your molecule by placing a reaction arrow. You can place the reaction arrow in any position, pointing in any direction. The structures behind the arrow will be considered Reactants, structures along the arrow Agents, and structures in front of the arrow as Products.

MarvinSketch will determine if the reaction is chemically valid. The existence of reaction errors is denoted by a red box around the arrow. This option can be turned on or off using the Edit > Preferences box.


MarvinSketch allows you to set a map label on any atom in the molecule. Map labels are useful because they remain constant, unlike atom indexes, which can change as the molecule is altered. Atom mapping can be very useful when drawing reactions. It allows you to specify that specific reactant atoms will become specific product atoms. You can assign the same free map number to both of these atoms by pressing the Reaction Button on the toolbar, then drawing the arrow from the first atom to the second one. You also can select a Map for an atom from the Atom Pop-up Menu, or else you can map selected atoms with unique map numbers from the Edit Pop-up Menu. You can also use the shortcuts M1, M2, ... to assign map labels, M0 to remove map labels, M= or M+ to assign unique map numbers.


MarvinSketch allows you to change an atom into one of its isotopes using the Atom Pop-up Menu.

E/Z Feature

By choosing View > Misc > E/Z Labels , you can toggle the display of absolute double bond stereoconfiguration labels. Bonds known to have an (E) or (Z) configuration will be marked as such.


MarvinSketch has a rich collection of features related to abbreviated groups.

Predefined Abbreviated Groups

A number of predefined S-groups are available in MarvinSketch. The complete set is listed under the Groups menu in the Periodic Table. These groups are also available as shortcuts. Select a group via the Groups menu or a shortcut, then move the mouse into the canvas and place the group by clicking on the desired location.

User-Defined Abbreviated Groups

To create a new group, first draw the structure on the canvas. Then, select what you wish to include in the group and choose Edit > Groups > Create. A dialog box will appear, prompting you to name your new group.

S-Groups and My Templates

User-defined groups are, by default, session-only. To retain a group for future use, add it to My Templates. This will also make the group available in the Groups menu or as a shortcut.

Working with Groups in the Molecule

Group manipulation functions are available through the Edit > Groups submenu and by right-clicking on an existing group.
Choosing Contract will contract a group to its abbreviation. To contract all groups in the molecule, choose Edit > Groups > Contract.
Choosing Expand will display the full structure. To expand all groups in the molecule, choose Edit > Groups > Expand.
Selecting Ungroup will remove all abbreviated groups from the molecule. The structures will remain, but will no longer be associated with their abbreviations. You will be unable to Expand/Contract these structures.
To add or remove an Attachment Point, right-click on an atom within the group and select the Group > Attachment Point checkbox.

Working with Radicals

MarvinSketch allows you to specify that an atom in the molecule is a radical. This functionality is available via the Atom Pop-up Menu.
To change an atom into a radical, right-click on it to access the Atom Pop-up Menu. Select the type of radical from the Radicals submenu. A radical symbol will appear next to the atom and a valence check will be run with errors highlighted.

Query Guide

The JChem query guide provides more detailed information on how to use query structures created in MarvinSketch with Jchem's query functionality. The following are some of the query building features available in MarvinSketch.


MarvinSketch allows you to specify R-groups within your molecule. These R-groups can be very useful in Markush structure queries. An R-group is a variable representing a user-defined list of structures. Using R-groups in a query structure can allow you to quickly search for a wide range of substructure hits using only a single query.
You can set or change the R-group label of a molecule node from the Atom Pop-up Menu.
To define the set of structures that are represented by an R-group label, select the structures you wish to include. Then, select the corresponding label from the Periodic Table or use one of the R-group Shortcuts.

Atom Lists

MarvinSketch allows you to add Atom List query atoms to your molecule. An Atom List is a user-defined list of elements included in a query structure, any of which will produce a hit if found in the target.

You can add Atom Lists to your molecule through the Periodic Table. To add an Atom List to the molecule, select the Atom List button, then select the elements you wish to include in the list. Move the mouse into the canvas and click to add a query atom representing this atom list.

Not Lists

A Not List is a query atom that allows you to define a list of elements that should not be included in the target structure. If an atom within the query structure is set as a Not List, then the atom in the same position within the target structure can be any atom that is not on the list to produce a hit.
To add a Not List to the molecule, select the Not List button in the Periodic Table, then select the elements you wish to include in the list. Move the mouse into the canvas and click to add a query atom representing this not list.

Generic Atoms

Generic atoms can be added to include a wide range of elements in a query structure. Currently, MarvinSketch supports two types of generic atoms: Any and Hetero
If an atom within the query structure is designated as "Any", any atom at this position in the target structure will produce a hit.
If an atom within the query structure is designated as "Q", then the atom at this position can be any heteroatom (i.e. any atom except hydrogen or carbon) and it will produce a hit.
To add a generic atom to the molecule, select one of the generic atom types from the Periodic Table and place it on the canvas with the mouse.

Atom Properties

You can define the chemical neighborhood for an atom within a query structure. MarvinSketch allows you to set properties, such as hydrogen count, valence count, ring size, and aromaticity, which must be matched by the corresponding atom in the target structure to produce a hit.
To set or change atom properties, select an atom property button from the Periodic Table. To apply this property, click on the desired atom.

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