Features

Overview of editor

Marvin Pro is equipped with a Top toolbar giving place to basic editing options such as the Undo and Redo, Zoom and Text editing. In addition, this is the place to find chemical services to Calculate chemical properties, Clean structures, switch between Aromatic and Kekulé representation of aromatic systems, calculate CIP stereodescriptors, show Explicit hydrogen atoms, Import structures easily and manage the Export of the content of the canvas into images and files.

The Left toolbar is the place of the main editing and Chemical drawing tools, starting with Selection and Erase, followed by a wide range of Chemical bonds, Templates, Atom toolbar, Markush,Query Tools and Electron tools. The Shapes, Text tool and Scribble line support the creation of unique, publication quality drawings. In addition, Marvin Pro provides a wide set of Arrow types and the Map reaction atoms feature to support the drawings of various chemical transformations.

At the top left corner of the application the Main menu can be found, which, above many other options, gives access to the editor Settings. The Context menu can be accessed from the canvas area to organize certain features and editing options, including Molecule properties, Atom properties and Bond properties, which are also available from the Main menu. The display of Atom numbers, the Duplication of selected objects, their Alignment and distribution and the order of layers can also be set from the Context menu.

General tools

Selection tools

Icon	Name	Shortcut
	Rectangle Selection	Esc
	Lasso Selection	Esc

The editor supports two selection modes: Rectangle Selection and Lasso Selection. The default mode is the Rectangle Selection. Can be used for both single (click) and multiple (drag) selections. Alternatively, double-clicking can be used to select a complete structure.

The selection tool mode affects the behavior of other tools including the Erase, Define RGroup, Variable attachment and Color tool.

By default, Marvin Pro uses the chemical selection scheme. This means that during selection dragging, it is not possible to select a bond without its atoms. To select a bond without the atoms, hold the Ctrl key and click the bond or start dragging with the selection tool.

Additional useful shortcut: Ctrl/Cmd + a selects the content of the canvas.

Erase

Icon	Shortcut
	Delete or Backspace or fn + Backspace

The Erase tool removes selected objects. Pressing the shortcut when hovering over an object will delete it. Otherwise, when used over an empty part of the canvas, the shortcut will take the tool in hand. Can be used for both single (click) and multiple (drag) selections.

Undo/redo

Icon	Name	Shortcut
	Undo	Ctrl/Cmd + z
	Redo	Ctrl/Cmd + y

Undo revokes the last editing step. The Redo button is inactive until the Undo button is clicked. It restores the last undone editing step.

Zoom

Icon	Shortcut
	Ctrl/Cmd + scrolling

The default Zoom value is 100%. The minimum value is 10% and the maximum is 500%. Zoom can be set from the top toolbar dropdown menu at predefined values or by using the plus and minus buttons.

Fit to canvas sets a zoom factor that lets you view the contents of the whole canvas.

Fit to selection sets a zoom factor that makes the selected structure fill the viewport.

Attach data

Icon	Name
	Attach data...

The Attach data tool offer the opportunity to attach arbitrary textual information to chemical structures, including complete molecules and fragments. This data may include search conditions in queries.

Having a selection on the canvas that includes no more than one chemical structure, the Attach data dialog can be opened from the Context menu. It is mandatory to fill out the Name and Value fields to create an Attached data, the Unit field and the Query operator are optional, the latter being none by default. The input fields accept any text or numbers. The Query dropdown menu has the following options: none, =, <, >, <=, >=, <>, between, like, contains. For more information, see Query guide.

As the Attached data is placed on the canvas, it appears on the top right corner of the structure. Hovering either the label or the structure, a purple highlight feedback appears on the included structure.

The attached data can be edited any time by opening the Context menu -> Edit attached data dialog from any part of the included structure or the data label.

Clean up reaction

Selected reactions can be cleaned using the Clean up reaction action from the selection's Context Menu. As a result, the Reaction components, i.e. starting materials, products, plus signs, reaction arrow, reaction agents and reaction conditions are aligned and distributed.

This action is only available if at least an arrow and a chemical structure is selected. The Clean up reaction is only available if the selection only contains one reaction and only reaction components.
Reaction components can be chemical structures and textboxes if their middle point overlaps with the plain of the arrow. Otherwise, chemical structures are either considered starting materials or products based on their relative position compared to the arrow and the textboxes are considered ineligible components.

Copy as

Icon	Shortcut
	Ctrl/Cmd + k

The contents the canvas can be copied by selecting the desired elements then accessing the Copy as function either through the selection's Context menu or through Menu > Copy as. Copying in the following formats is accessible right away:

MRV
CXON
SVG

The Copy as other format offers a wider range of formats which are listed in the Export section.

Duplicate

Icon	Shortcut
	Ctrl/Cmd + c followed by Ctrl/Cmd + v

The selected object (atom, bond, structure, fragment, text or image) may be duplicated on the canvas from its Context menu. Using the Ctrl/Cmd + c shortcut will copy the selection to the clipboard.

Bring to Front/Send to back

Icon	Name	Shortcut
	Bring to front	-
	Send to back	-

If a selected object overlaps with other elements on the canvas, from its Context menu you may move it behind or in front of all of them, making editing more convenient.

Align

When selecting multiple objects on the canvas, it is possible to Align them next to each other or Distribute them in even distances horizontally or vertically.

Icon	Name
	Left
	Center
	Right
	Top
	Middle
	Bottom
	Distribute horizontally
	Distribute vertically

Image

Icon	Name	Shortcut
	Insert image	Ctrl/Cmd + i
	Crop image	-

Clicking on the Image icon will open a file browser window. Then, you can select any image file from your local system to add it to the contents of the canvas.
Selected images can be cropped using the Crop image tool, accessible either from the top toolbar or the Context menu or by clicking twice on the image.

Crop mode can be left by pressing Enter, Esc, the Crop image button or by clicking on an empty part of the canvas.

Color

Icon	Shortcut
	-

With the Color tool, you can change the color of an object (clicking) or every canvas object at once (dragging). Images are excluded. Opposite to the other specific coloring tools, Color is generic and will affect all eligible objects on the canvas.

Scribble Tool

Icon	Shortcut
	-

By using Scribble tool, you can jot down ideas or add complementary sketches to your canvas.

The scribble can be selected, dragged, rotated, and resized. Upon selection the Line Color tool appears on the top toolbar. It is also possible to change its color with the Color tool.

Chemical Drawing tools

Bonds

The following bond types are accessible in Marvin Pro from the left toolbar:

Icon	Name	Shortcut
	Single	1
	Double	2
	Triple	3
	Up wedge	w
	Down wedge	h or Shift + w
	Wavy	y
	Hashed	Shift + h
	Dashed	d
	Bold*	-
	Dative	-
	Aromatic	-
	Cis or trans	x
	Double C/T or unspecified	-
	Single or double	12
	Single or aromatic	14
	Double or aromatic	24
	Any	Shift + a
	Coordinate	-

*Besides acting as the other bond tools, Bold bond will not overwrite Double and Aromatic bonds but turns them into their bold versions.

Bond color is adjustable, see Color tool.

Holding shift while hovering over an atom with the bond tool in hand offers another angle for placing the bond.
Shortcuts only works in bond context. Otherwise, press the shortcut key over an empty part of the canvas to take in hand.
When a bond is selected on the canvas, the top toolbar expands, enabling bond coloring.

Coordinate bond

The Coordinate bond can be placed on the canvas by selecting a group of atoms together with a target atom. If no target atom is selected, the end of the bond is considered a carbon atom. Only one target atom can be selected at once but the selection may contain multiple atom groups. Hovering over any included atom or the bond triggers a purple highlight feedback on the coordination structure.

The tool uses the current selection method (i.e. rectangle or lasso).

Chain tool

Icon	Shortcut
	-

The Chain tool facilitates the drawing of longer chains. After taking the tool in hand click and drag on the canvas to draw alkyl chains. During dragging, the number of chain members is shown at the tooltip.

Templates

The following templates are accessible by default in Marvin Pro from the left toolbar:

Icon	Name	Shortcut
	Benzene	a
	Cyclohexane	6
	Cyclopentane	5
	Cyclobutane	4
	Cyclopropane	v
	Cyclohexane chair 1	0
	Cyclohexane chair 2	9
	Cycloheptane	7
	Cyclooktane	8
	Cyclopentadiene	z

By pressing the shortcut key, the corresponding template gets in hand. In bond context, the shortcut action merge the template to the structure on the canvas.

Shortcuts 3, 6 and 7 are working in atom context as well.

Atoms

Typing an atom label over the canvas will take the appropriate element into hand, however, doing it over an atom will exchange it automatically.

The following atoms can be accessed quickly from the Left toolbar -> Atoms combo box:

Other atoms can be selected by clicking the Periodic Table button. On the opening dialog it is possible to create Atom list and NOT list, see Query tools. Also, aliases can be created using the Text tool.
The following atoms can only be placed on the canvas from the Periodic table as they will be represented as Abbreviated groups if created by typing or using the text tool: Actinium - Ac, Neptunium - Np, Cerium - Ce, Praseodymium - Pr, Americium - Am.

When an atom gets selected on the canvas, the following new options appear on the top toolbar:

Font type and size, which will affect the atom label and the atom properties added to the atom.
Style elements (Bold, Italic, Underline)
Superscript and Subscript
Formula tool: Using the Formula tool, the input text is automatically turns to Chemical formula. Existing texts can also be transformed to Chemical formula.
Text color can be used to set colors to atom labels and properties. Also, CPK coloring can be used to colorize atoms.

Markush tools

The Markush tools are accessible from the left toolbar, containing the following tools.

RGroup

Icon	Shortcut
	r

The RGroup tool lets you place R-group labels on the canvas or on structures with a single click. It is also possible to add the labels by dragging the mouse, it is useful when you would like to sprout the label from a structure. Marvin Pro starts the numbering with R1, then automatically increases the number. By using the Text tool, the labels can be rewritten.
In case having at least two bonds connecting to the R-group label and having a corresponding definition, the bonds around the label are numbered in the order of placement indicating their connection pattern on the definition structure.

The visibility of the ligand order can be changed in Settings. Turning the Show R-group attachment order on/off will also affect the numbers on the R-group definitions and the Image export.

Define RGroup

Icon	Shortcut
	-

The Define RGroup can be used to assign selected structures to the R-group labels. Similarly to the RGroup tool, the numbering starts with R1, then the number is automatically increased.
In case of having at least two RGroup Attachments on a definition structure, the attachment bonds are numbered in the order of placement indicating their connection pattern on the parent structure.

The visibility of the ligand order can be changed in Settings. Turning the Show R-group attachment order on/off will also affect the numbers around the R-group labels and the Image export.

RGroup Attachment

Icon	Shortcut
	-

The RGroup Attachment bond visualize the point of attachment between a definition and the parent structure.

Variable attachment

Icon	Shortcut
	-

The Variable attachment tool is the Marvin Pro version of the Position variation known from Marvin Sketch and Marvin JS.
It enables the representation of atoms and groups connecting to various points of a parent structure. The involved atoms and bonds are highlighted with a patch and give hover feedback.

The representation of the highlight patch can be changed in Settings. In the Variable attachment submenu the reprsentation may be set to Color highlight, Gray highlight, or No highlight.

The Variable attachment bond may be moved and the length and angle may be modified by dragging the inside endpoint of the bond. The outside end of the bond may be edited with arbitrary atoms and complex structures.

The editor recognises if there is a Variable attachment on the canvas and offers to include the highlight patch during Image export. The default setting may be changed in Settings, in the Variable attachment submenu.

Charge

Icon	Name	Shortcut
	Increase Charge	+
	Decrease Charge	-

Charge can be set on atoms by taking the Increase Charge and Decrease Charge tools in hand and clicking on the atom. Any additional click will either increase or decrease the charge.
Charge can also be set from the Main menu -> Atom submenu and the Context menu, see Atom properties.

The display of Charge can be set from Settings.

Borders and lines

The following shapes are accessible in Marvin Pro from the left toolbar:

Icon	Name
	Rectangular border
	Ellipse
	Line
	Dashed line

When a shape is placed on the canvas, the following new options appear on the top toolbar:

Line Color: By using this tool, the color of the object’s outline can be specified.
Fill Color: By using this tool, the fill color of the object can be specified. The opacity of the fill color can also be set.
Line Weight: By using this tool, the boldness of the lines can be specified in pixels.

Holding shift during placing a Rectangular border or Ellipse enables the creation of squares and circles. Also, when resizing these objects, holding shift will keep the original ratio of the shapes.

Brackets

The following Brackets can be drawn in Marvin Pro from the left toolbar:

Icon	Name
	Square bracket
	Round bracket
	Curly bracket

The Square brackets and Round brackets can be used to create S-groups.

S-groups

When a bracket is placed around a chemical structure, an input field pops up enabling to add text that will appear in the bottom right corner of the bracket. Based on the structure and the input value, the bracket will be automatically categorizted into a repeating unit type. The value can be edited anytime by double clicking on the bracket or the label.
The following repeating unit types are available in Marvin Pro:

Repeating unit type	Value conditions	Structural conditions
Link node	Range of integers starting from 1 (e.g. 1-4)	The bracket is placed around one atom that has only two connecting bonds
Repeating unit	Range of integers* and integer (e.g. 0-4; 1-3, 6-8; 3-5, 8; 2, 4-6)	The bracket is placed around a fragment with either 1-1 or 2-2 bonds crossing both brackets
SRU polymer	One letter (e.g. n; m)	The bracket is placed around a fragment with either 1-1 or 2-2 bonds crossing both brackets
Multiple group	Integer (e.g. 4)	The bracket is placed around a complete molecule, a fragment with 1 bond crossing both or only one of the brackets, a fragment having 2-2 bonds crossing both brackets
Custom bracket	Any input is accepted	No structural restrictions

*Range can start from 0.

If the bracket does not fit into any repeating unit types, it will be categorized as a Custom bracket.
Hovering either the bracket or the structure, a purple highlight feedback appears on the included structure and a tooltip shows the Repeating unit type.

Opening the Context menu of the bracket the Bracket style can be switched between Square and Rounded. Also, in the case of Repeating units and SRU polymers, the following repeating patters can be set that will appear at the top right corner of the bracket:

Repeat pattern	Label*
Head-to-tail	-
Head-to-head	hh
Either/unknown	eu

*The default label is Head-to-tail, which is not displayed on the bracket.

The color of the bracket can be specified using Line Color from the top toolbar or the Color tool.

Graphical brackets

When a bracket is placed on the canvas and no chemical strcuture is involved, it is considered a graphical bracket. The color of the bracket can be specified using Line Color from the top toolbar or the Color tool and its size can be customized using the edit points appearing upon selection.

Holding shift during placing Brackets enables the creation of square shaped objects. Also, when resizing brackets, holding shift will keep the original ratio of the shapes.

Reaction components

Arrows

The following Arrows are accessible in Marvin Pro from the left toolbar:

Icon	Name
	Single
	Equilibrium
	Unbalanced equilibrium
	Resonance
	Open
	Dashed
	Crossed
	Hashed
	Retrosynthesis
	Curved
	Half-headed curved
	Circular
	Single electron flow
	Double electron flow

The type of the arrows placed on the canvas can be changed from the Context menu. They can also be switched to Lines. The only exceptions are the Single and Double electron flow arrows. When an Arrow is placed on the canvas, the color of the object’s outline can be specified using Line Color from the top toolbar.

Holding shift during placing Circular arrow enables the creation of circle shaped arrows. Also, when resizing arrows, holding shift will keep the original ratio of the object.
The direction of the Unbalanced equilibrium arrow can be switched by rotating the arrow 180°.

Electron flow arrows

The Single and Double electron flow arrows can be used to represent electron movements on the canvas. They are located on the left toolbar in the Arrows subtoolbar. After picking up the tool, the arrow can be created by clicking on an eligible starting point and either dragging the arrow to the target (creating a more rounded arrow) or just clicking on it (creating a more flat arrow). Clicking on the arrow reveals an edit point that can be used to change its curve.
The following objects are eligible starting points for the electron flow arrows:

Starting point	Single electron flow	Double electron flow
Monoradical	Can host one arrow	n/a
Diradical singlet	Can host two arrows	Can host an arrow
Lone pair	Can host two arrows	Can host an arrow
Bond	Can host two arrows	Can host an arrow

The electron flow arrows can target any natural atoms and any type of bonds and can be created inside a molecule or between the atoms and bonds of different molecules. Atom lists, NOT lists, Query atoms, Homology groups, RGroup labels, contracted Abbreviated groups and Aliases, however, are not eligible targets for electron flow arrows.

Plus sign

Icon	Shortcut
	-

Plus sign can be accessed from the left toolbar. Placing a Plus sign between reagents or products indicate that they participate in a chemical reaction.
When an PLus sign is placed on the canvas, the color of the object’s outline can be specified using Line Color from the top toolbar.

Imported reactions that do not contain plus signs, are automatically replaced by the editor.

Map reaction atoms

Icon	Shortcut
	-

The Map reaction atoms tool enables the creation of manual mapping between chemical structures. When having the tool in hand, clicking on an atom and dragging towards another atom on a different molecule creates a mapping. Hovering over a map number reveals all of its connections displayed by blue lines.

Starting a mapping from an atom that already has a number will overwrite the target atoms map number.
Map numbers cannot be edited manually.

Electron tools

Add radical

The Add radical tool can be used to equip atoms with radicals by click, giving access to monovalent, divalent triplet and trivalent quartet radicals. Divalent singlet radical can be created by selecting Context menu -> Radical -> Diradical and adding another radical using the Add radical tool enables the creation of trivalent dublet radicals.
If having three radicals on an atom, using the tool sets the radical state to Off, removing the unpaired electrons.

Add lone pair

The Add lone pair tool can be used to add one to four lone pairs around an atom. When having four lone pair around an atom, upon clicking a fifth time on it, all lone pairs are removed. The position of a lone pair can be customized by grabbing and relocating it manually when having the selection tool in hand.

Text tool

Icon	Shortcut
	-

The Text tool is available from the left toolbar. Clicking on the canvas with the Text tool in hand opens a text field for input. Changes made to the text field can be saved by either clicking on an empty part of the canvas or pressing Esc. Enter can be used for inserting line breaks. When a text field is edited, the following options appear on the top toolbar:

Font type and size
Style elements (Bold, Italic, Underline)
Superscript and Subscript
Formula tool: Using the Formula tool, the input text is automatically turns to Chemical formula. Existing texts can also be transformed to Chemical formula.
Symbols
Text color
Highlight color
Align options (Left, Center, Right)

Abbreviated groups

Icon	Name
	Expand
	Contract
	Ungroup

There are two ways to add the Abbreviated groups to the canvas. In both cases, you need to modify an atom already present. You can either hover the cursor over this atom and start typing (in this case, a drop-down menu appears with possible group names) or use the Text tool to rewrite an atom with a group’s name (no drop-down menu appears to guide you in this case).

Transforming abbreviated groups

Once an Abbreviated group is on the canvas, it can be expanded from its Context menu to show the underlying structure. The Expand command also cleans and selects the structure.
As long as the Abbreviated group is unchanged it can be contracted from its Context menu. Otherwise, upon modification of the structure, it is automatically ungrouped and cleaned.
It is also possible to manually ungroup an abbreviated group through its context menu by using the Ungroup command.

Display of abbreviated groups

Hovering any part of the expanded abbreviated structure, a purple highlight feedback appears on it enclosed in a bracket preview and showing the contracted label on the bottom right corner. The purple dots indicate the abbreviated group’s attachment points to the parent structure.
The attachment points of multiple attachment point abbreviated groups are organized in order indicated by their cardinal numbers which can be revealed on the tooltip by hovering over them in expanded state. When connecting bonds to a contracted abbreviated group, the attachment points are used up starting with the attachment point 1 followed by 2, etc.

Merge and split components

Icon	Name
	Merge components
	Split components

When multiple chemical structures are selected the Merge components action appears in the selection's Context menu. Merged components are handled as one molecule e.g receives a single Molecule level stereo label, gets complete selection to a double click and the Formula and molweight selection gives a single data box for a complete selection. This feature offers the opportunity to handle salts and other molecular groups in Marvin Pro.
Hovering any part of the merged structure, a purple highlight feedback appears on every member of the group enclosed in a bracket preview.
The Split components action is available from the merged components Context menu and separates the merged components to individual chemical structures.

The Merge and Split components actions are available if the selection contains only chemical structures.

Stereochemical representations

Chan-Ingold-Prelog (CIP) stereodescriptors

The CIP stereodescriptors can be turned on from the top toolbar, using the Show Stereo button.

Molecule stereo

In Marvin Pro, the Molecule stereo labels can be assigned to any chiral molecules from its Context menu. The default setting is Absolute and it can be changed to Mixture. In the Stereochemistry options dialog, the visibility and name of the stereochemical flags can be set.
There can only be either a Molecule stereo flag or Enhanced stereo flags assigned to a molecule. If switching from the enchaned stereo representation to molecule stereo flag, the enhanced stereo information is lost. Using the Undo and Redo buttons restores the previous stereodescriptors.

Enhanced stereo

Enhanced stereo descriptors can be assigned to chiral atoms. By default, all chiral atoms are considered abs and this label can be changed from the Context menu to and and or labels. There can only be either a Molecule stereo flag or Enhanced stereo flags assigned to a molecule.
When having multiple chiral centers in the molecule and turning from Molecule stereo label to enhanced labels, the remaining chiral atoms are automatically equipped with enhanced labels by the following rules:

Molecule stereo label	Selected atom enhanced stereo label	Remaining chiral atoms enhanced stereo labels
Absolute	abs	abs
Absolute	and/or	abs
Mixture	abs	and1
Mixture	and/or	and1

Geometric transformations

Resize

Graphical objects and images can be resized using the edit points appearing upon selection. This option is available for Borders and lines, Brackets, Arrows, Plus sign, Text box, Images and Scribbles.

Rotate in 2D

When an object is selected the appearing rotate icon indicates that it can be rotated in 2D. This option is available for molecular structures, Borders and lines, Brackets, Arrows, Images and Scribbles.

Mirror & Rotate

Icon	Name	Shortcut
	Mirror horizontal	Alt/Option + h
	Mirror vertical	Alt/Option + v
	Rotate horizontal	-
	Rotate vertical	-
	Mirror group	-
	Rotate group	-

When selecting chemical structures on the canvas, the Mirror & rotate submenu appears in the Context menu. The Mirror/Rotate horizontal and Mirror/Rotate vertical actions mirror or rotate the selection in 180° around a horizontal or vertical axis in the plane of the drawing. This feature is feasible on complete molecules and fragment selections.
The Mirror group and Rotate group options appear when the selected fragment is only connecting to the rest of the structure through one connection point. In that case, the connecting bond acts as the axis for the geometrical transformation.

The mirror transformation results in the inversion of the stereocenters. The rotate transformation results in the retention of the stereocenters.

Query tools

Query Atoms

The following Query Atoms are available from the left toolbar:

Icon	Name
A	Any non hydrogen
AH	Any atom
Q	Hetero atom
QH	Hetero atom or hydrogen
M	Metal
MH	Metal or hydrogen
X	Halogen
XH	Halogen or hydrogen

Homology groups

Icon	Name
	Homology groups

In the left toolbar, the following Homology groups are available from the opening dialog. The definitions can be found at the Homology groups page.

Name	Abbreviation
Actinide	ACT
AlkaliMetal	AMX
Alkenyl	CHE
Alkyl	CHK
Alkynyl	CHY
AnyAtom	-
AnyGroup	XX
Aryl	-
Carboalicyclyl	CYC
Carboaryl	ARY
Carbocyclyl	-
CarbonChain	-
Cyclyl	-
Fusedheteroalicyclyl	-
Fusedheteroaryl	-
Fusedheterocyclyl	HEF
Haloalkyl	-
Halogen	HAL
Heteroalicyclyl	-
Heteroaryl	-
Heterocyclyl	-
Heteromonoalicyclyl	HET
Heteromonoaryl	HEA
Heteromonocyclyl	-
HeteroSubstitutedAlkyl	HSA
Hydroxyalkyl	-
Lanthanide	LAN
Metal	MX
OtherMetal	A35
Protecting	PRT
RingSegment	-
TransitionMetal	TRM
UnknownGroup	UNK

Atom lists/NOT lists

In the Periodic table dialog, Atom lists and NOT lists can be created and assigned as an atom label.

Query bonds

The list of Query bonds available in Marvin Pro are listed in Bonds.

Atom query properties

The following Atom query properties are available in Marvin Pro:

Name	Abbreviation	Eligible values
Total H count	H	Empty, 0-99
Implicit H count	h	Empty, 0-99
Connections	X	Empty, 0-99
Smallest ring size	r	Empty, 0-99
Ring count	R	Empty, 0-99
Unsaturated	u	Yes/No
Ring bond count	rb, rb*	Off, As drawn, 0-99
Substitution count	s, s*	Off, As drawn, 0-99
Aromaticitiy	a, A	Off, Aromatic, Aliphatic

Valence

In Marvin Pro custom valence values can be assigned to atoms from the Main menu -> Atom -> Valence submenu or the Context menu. There is a range of predefined values from 0 to 8 that can also be assigned in multiselection of the same type of atoms. Custom values can also be added for individual atoms.

Bond properties

When there is a selection on the canvas that includes bonds, Bond properties become accessible from the Main menu -> Bond submenu or the Context menu.

Topology

The Topology value is Undefined by default and may be switched to In ring or In chain.

Setting Topology is enabled in mixed selection as well.

Reacting center

The Reacting center value is Undefined by default and the following values may be set.

Icon	Name
-	Undefined
	Center
	Make or break
	Change
	Make and change
	Not center

Setting Reacting center is enabled in mixed selection as well.

Atom properties

When there is a selection on the canvas that includes atoms, the Atom properties become accessible from the Main menu -> Atom submenu or the Context menu.

Charge

The Charge can be selected from predefined values or custom values can be used by clicking on the "..." icon. The selected values can be modified using the Charge tool.

Setting Charge is enabled in mixed selection as well but custom charge can only be assigned in single selection.

Enhanced stereo

The Enhanced stereo labels can be assigned to any chiral atoms. The toggle button in the submenu is a global on/off button for Stereochemical labels on the canvas.

In multiselection, it is possible to set enhanced stereo labels, choosing from the predefined label set.

Isotope

For natural elements, an Isotope may be selected. The default setting is Off indicating a natural mixture of isotopes. Predefined values may be selected from the submenu or custom values can be added by clicking on the "..." icon.

In multiselection, the Isotope option is only available when selecting atoms of the same type.

Periodic table

The Periodic table tool is available from the Atoms combo box as well.

Query properties

The following Query properties are eligible in Marvin Pro for atoms:

Input fields accepts integers between 0 and 99. This tool is only available in single selection

Radical

The default setting or Radical is Off and it can be switched to Monoradical or Diradical from the Context menu.
Also, on the left toolbar, the Electron tool can be used to add more radicals to an atom.

Assigning radicals is enabled in mixed selection as well.

Valence

Custom Valence values can be assigned to atoms, see Atom query properties.

Atom numbering

It is possible to display unique atom numbers on the canvas. If the Enable atom numbers toggle button is turned on from Main menu -> Settings, then the Show atom number toggle button will be available from the Context menu. Turning Show atom number On will display the unique numbers assigned to atoms.
The atom numbers can be selected and moved to custom locations around the corresponding atom label and their color can be set individually from the top toolbar or by using the Color Tool.

This display option is enabled in mixed selection as well.

Chemical calculations & services

Formula & Molweight

Icon	Shortcut
	Shift + m

Activation of the Formula & Molweight tool calculates the formula, molar mass and exact mass of selected structures or fragments. The calculation automatically updates while dragging the cursor during selection. The databox can be persisted on the canvas using the pin button. Structural changes affecting the selection will update the data content of the pinned box. Upon clicking the pin button again or by chemical modifications of the selected fragment, the box disappears.

Clean

Icon	Shortcut
	-

Cleans the selected object. If nothing was selected, the cleaning is applied to the whole canvas.

Aromatize/Dearomatize

Icon	Shortcut
	-

The Aromatize service transforms the molecule from Kekulé representation to aromatic representation by using the general aromatization method.
The Dearomatize service transforms the molecule from aromatic representation to Kekulé representation. (This method does not check by default if Hückel's rule is valid.)
Pressing the button successively, the function converts the structure from Kekulé to aromatic form back and forth. If there is a selected aromatic ring on the canvas, the aromatize and dearomatize method works only for the selected structure.

Show stereo

Icon	Shortcut
	-

The Show stereo service assigns the R or S label to chiral centers and the E or Z label to unsymmetrical double bonds.

Add or remove explicit H

Icon	Shortcut
	-

Adds or removes hydrogen atoms to/from the selected structures or fragments. Without selection, changes apply to every atom on the canvas.

Name to structure

The Name to structure service can be accessed as a free text field from the upper toolbar for importing structures based on their names. IUPAC, traditional names of chemicals, Drug names, Acronyms SMILES, SMARTS and CAS Registry Numbers® are supported.
For more information about the underlying technology, see Name to Structure.

Valence error

In Marvin Pro, the Valence error is indicated by a red, dashed ellipse around the atom label.

The visibility of the valence error can be changed in Settings.

Import/Export

Import

Open

The Open dialog can be reached from the Main Menu to open files. Marvin Pro supports the CXON and MRV chemical file formats and JPG, PNG, SVG and BMP image file formats for import.

The Name to structure field supports a wide range of chemical notation languages for import.

Insert

The Insert dialog can be reached from the Main Menu to open image files. The listed image file formats are supported by Marvin Pro. Also, the Image button from the left toolbar opens the Insert dialog.

The Insert dialog can be opened using the Ctrl/Cmd + i shortcut as well.

Export

Download as file

Icon	Name
	Download
	Download as file

The Download button enables the export of the canvas in a chemical file format. Marvin Pro supports the following file formats.

CXON
MRV
MDL Molfile
SMILES
SMARTS
InChI
InChIKey
MDL Molfile V3000
CDX
SKC
MDL SDF
MDL RDF
MDL RXN

The Copy as option also offers PNG and SVG image formats.

Pressing the Export button downloads the data in file format, while the Source button copies the data onto the clipboard.
Download can also be reached from the Main Menu.

Download as image

Icon	Name
	Download as image

The Download button enables the export of the canvas in an image file format. Marvin Pro supports the export of images in JPG, PNG, SVG and WebP. The width and height of the exported can be set.
If there is an active selection on the canvas, the Selected area only options enables the export of the corresponding part of the canvas.
In addition, if there is a Variable attachment on the canvas the Include variable attachment highlight option enables the export of the Variable attachment highlight.

Visibility settings

Stereochemical labels

The display and visibility of Stereochemical labels and descriptors can be set in Marvin Pro. The Show Stereo button assigns the R/S and E/Z descriptors to eligible atoms and bonds. From the Main menu -> Settings -> Stereochemistry options dialog, the visibility of molecule level stereochemical notations and atom level enhanced stereo notations can be set. Also the selective display of 'chiral' and 'not chiral' flags and their names can be changed from the dialog.

The following Chiral flag names are available:

Absolute
Chiral

The following Not chiral flag names are available:

Mixture
Racemic
Relative
Not absolute
Not chiral

The selected Chiral and Not chiral flag names are effective to the whole canvas.

The global visibility of molecule level and atom level chiral flags can also be set from the Context menu -> Enhanced stereo submenu and, if complete molecules are selected, from the Context menu -> Stereo submenu.

Charge

The display of Charge may be set to Default or Circled from Main menu -> Settings -> Charge submenu.

Variable attachment

The display of the Variable attachment highlight color may be set to Color highlight or Gray highlight from the Main menu -> Settings -> Variable attachment submenu. Also, the general visibility of the highlight patch can be turned On/Off using the Show variable attachment highlight toggle button in Main menu -> Settings.

Molecule visualization

The display of chemical structures on the canvas may be set from the Main menu -> Settings -> Molecule visualization dialog to the following visibility options:

No implicit hydrogens
Skeletal (default)
Implicit hydrogens on terminals and heteroatoms
Heavy atoms without implicit hydrogens
Structural

Style settings

From the Main menu -> Settings -> Style settings dialog, the following structural display options can be set:

Bond spacing -> set the distance between double and triple line bonds in percentages of the bond length.
Fixed length -> set the bond length between the atoms in points.
Width -> set the bond width in points.
Bold width -> set the bold bond width in points.
Margin width -> set the amount of space around the atoms that is masked out of the connecting bonds in points.
Hash spacing -> set the distance between bond hashes in points. Only affects the Down wedge bond and the Hashed bond.
Atom font and properties -> set the default font type for atom labels and atom and bond properties.
Atom label size -> set the default size for atom labels and atom and bond properties.

The effect of the modifications can be checked instantly on the dynamically changing example structure.
The applied settings will not affect the uniquely set atom fonts and label sizes on the canvas.

CPK coloring

CPK coloring of atoms can be turned On/Off using the Main menu -> Settings -> Use CPK coloring toggle button.

Atom numbering

In the Main menu -> Settings submenu, the visibility of the Atom numbering can be set by the Enable atom numbers toggle button. If turned on, the atom numbers can be displayed from the Context menu using the Show atom numbers toggle button. If the Enable atom numbers is turned off, the visibility toggle button is removed from the Context menu and the atom numbers become hidden. The assigned numbers are remembered by the editor and turning the toggle button back on will reveal the last set of atom numbers.

R-group attachment order

In the Main menu -> Settings submenu, the visibility of the RGroup ligand order around the RGroup labels and the RGroup attachments can be set using the Show R-group attachment order toggle button.

Valence errors

In the Main menu -> Settings submenu, the visibility of the Valence errors can be set using the Show valence errors toggle button.