Clean 2D > Clean in 2D

Calculates new 2D coordinates for the molecule.

Clean 2D > Clean and Arrange in 2D

Cleans the structure(s) and places them in the center of the canvas.

Clean 2D > Hydrogenize Chiral Center

Adds an explicit hydrogen atom to a chiral center having no terminal atoms when 2D cleaning is performed.

Clean 2D > Clean Wedge Bonds

Arranges the wedge bonds of the molecule in 2D.

Clean 3D > Clean in 3D

Calculates new 3D coordinates for the molecule. Clean3D builds up conformers of fragments from which the best, i.e. the lowest energy conformer is given back. The quality of the structures is measured by a simple energy function (Dreiding type molecular mechanics).

Clean 3D > Cleaning Method > Fine Build

Fine Clean3D builds up conformers of fragments to find low energy conformer. Leaves failed fragments intact.

Clean 3D > Cleaning Method > Fine with Hydrogenize

The build process always adds explicit hydrogens to the structures which are removed if not present in the original molecule. This option prevents the removal of extra hydrogen atoms, otherwise gives the same results than Fine build.

Clean 3D > Cleaning Method > Fast Build

Fast clean, which if fails, performs fine clean. It accepts any generated structure, and it is the default behavior of the Clean3D function.

Clean 3D > Cleaning Method > Build or Optimize

Builds 3D structure for non-3D molecules and just optimizes the 3D molecules with the Dreiding force field.

Clean 3D > Cleaning Method > Gradient Optimize

Optimizes with the Dreiding force field using the actual structure as starting geometry.

Clean 3D > Display Stored Conformers

Allows you to choose one of the possible conformer structures which were calculated via the Conformers plugin.

Directed Merge > Assign Atoms

Chooses the atoms of the fragments to be merged.

Directed Merge > Merge

Merges the fragments at the atoms set.

Add > Add Explicit Hydrogens

Adds explicit H atoms instead of the current implicit ones. Explicit hydrogens are displayed with atoms joining its neighbor while implicit hydrogens are displayed by atom symbols only.

Add > Data

Attaches data like stoichiometry coefficient to the molecule.

Add > Absolute Stereo (CHIRAL)

Sets chiral flag for the molecule.

Add > Multi-Center

Adds 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.

Add > No Structure

Places a No Structure label on the canvas.

Remove > Explicit Hydrogens

Removes explicit H atoms and increases the number of implicit hydrogens.

Remove > Data

Removes attached data from the molecule.

Remove > Absolute Stereo (CHIRAL)

Removes the chiral flag of the molecule.

Edit data

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

Edit properties

Bond properties can be edited from this menu.

Aromatic Form > Convert to Aromatic Form

Transforms the molecule to aromatic representation using the transformation method set.

Aromatic Form > Conversion Method > Basic

Basic aromatization method is described here.

Aromatic Form > Conversion Method > General

General aromatization method is described here.

Aromatic Form > Conversion Method > Loose

Loose aromatization method is described here.

Aromatic Form > Convert to Kekulé Form

Transforms the molecule to non-aromatic representation.

Group > Group

Creates a custom S-group, R-group or Repeating Unit with Repetition Ranges.

Group > Frequency Variation

Creates a Repeating Unit with Repetition Ranges.

Group > Merge Brackets

Creates a bracket that crosses two bonds.

Group > Edit Group

Modifies the properties of the selected group (restricted to 4 types: generic, component, monomer, mer).

Group > Contract Group

Contracts all groups to its abbreviations.

Group > Expand Group

Displays the full structure instead of the abbreviations.

Group > Ungroup

Removes all abbreviated group associations from the molecule.

Reaction > Merge Reactants

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

Reaction > Unmerge Reactants

Removes selected fragments from a previously merged reactant, product, or agent.

Mapping > Map Atoms

Inserts map numbers of the selected atoms.

Mapping > Manual Atom Map

Inserts map numbers manually

Mapping > Reaction Mapping Method > Complete

All atoms in the reaction are mapped.

Mapping > Reaction Mapping Method > Changing

Only those atoms are mapped that have changing bond. Either the bond order changes, or new bond is created, or bond is deleted. Orphan and widow atoms are included.

Mapping > Reaction Mapping Method > Matching

Maps all matching atoms in the reaction (Daylight style mapping). A reaction atom is called matching if it is not an orphan/widow atom: it exists on both sides of the reaction.

Mapping > Unmap Atoms

Removes map numbers of the selected atoms.

Attribute > 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 window.

Place Analysis Box

Places the Analysis Box containing the preset calculations.

Structure to Name > Place IUPAC Name

Inserts IUPAC Name onto the canvas.

Structure to Name > Generate Name

Generates IUPAC and/or Traditional Name.

Name to Structure

Opens the Source window in IUPAC Name format, and enables you to enter directly a IUPAC Name and convert it to structure.

Markush Enumeration

Generates a whole or a subset of the library of a generic Markush structure.

Check Structure

Checks and corrects chemical structures. See Structure Checker in MarvinSketch for more details.

Auto Check

Toggles auto checking of structures while drawing.