Features

    General tools

    Chemical drawing tools

    Stereochemical representations

    Geometric transformations

    Query tools

    Atom properties

    Chemical calculations & services

    Import/Export

    Visibility settings

    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 drawing area 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 drawing area 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
    Selection Icon Rectangle Selection Esc
    Selection Icon 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/⌘ + a selects the content of the drawing area.

    Erase

    Icon Shortcut
    Erase Icon 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 drawing area, 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 Icon Undo Ctrl/⌘ + z
    Redo Icon Redo Ctrl/⌘ + Shift + z

    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
    Zoom Icon Ctrl/⌘ + 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 drawing area. This feature can also be accessed using the Ctrl/⌘ + 1 shortcut.

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

    Attach data

    Icon Name
    Attach data icon 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 in the drawing area 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 added, 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 [Ctrl/⌘ + Shift + x] 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 if their middle point overlaps with the vertical plain of the arrow. Textboxes will be placed over and under the arrow if their bounding box is inside of the vertical plain of the arrow or overlaps with it Otherwise, chemical structures are either considered starting materials or products based on their relative position compared to the arrow and textboxes are kept at their original position.

    Copy as

    Icon Shortcut
    Copy Icon Ctrl/⌘ + k

    The contents the drawing area 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
    Duplicate Icon Ctrl/⌘ + d

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

    Bring to Front/Send to back

    Icon Name Shortcut
    BringToFront Icon Bring to front -
    SendToBack Icon Send to back -

    If a selected object overlaps with other elements in the drawing area, opening its Context menu makes it possible to move it behind or in front of all other objects, making editing more convenient.

    Align

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

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

    Image

    Icon Name Shortcut
    Image Icon Insert image Ctrl/⌘ + i
    CropImage Icon 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 drawing area.
    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 drawing area.

    Color

    Icon Shortcut
    Paint Icon -

    With the Color tool in hand, clicking on an object will change its color. If dragging in the drawing area, the Color tool will use the current selection method to colorize objects. Images are excluded. Opposite to the other specific coloring tools such as Text color and Line color, Color is generic and will affect all eligible objects in the drawing area.

    Scribble Tool

    Icon Shortcut
    Scribble Icon -

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

    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 Bond Icon Single 0 and 1*
    Double Bond Icon Double 2
    Triple Bond Icon Triple 3
    Up Wedge Bond Icon Up wedge w
    Down Wedge Bond Icon Down wedge h or Shift + w
    Wavy Bond Icon Wavy y
    Hashed Bond Icon Hashed Shift + h
    Dashed Bond Icon Dashed d
    Bold Bond Icon Bold** -
    Dative Bond Icon Dative -
    Aromatic Bond Icon Aromatic -
    Double Cis or Trans Bond Icon Cis or trans x
    Double Cis or Trans or Unspecified Bond Icon Double C/T or unspecified -
    Single or Double Bond Icon Single or double 12
    Single or Aromatic Bond Icon Single or aromatic 14
    Double or Aromatic Bond Icon Double or aromatic 24
    Any Bond Icon Any Shift + a
    Coordinate bond Coordinate -

    *The '0' hotkey tends to build rings and the '1' hotkey tends to build chains.
    **Besides acting as the other bond tools, Bold bond will not overwrite Double and Aromatic bonds but turns them into their bold versions.

    It is possible to select only bonds without the atoms they are connecting by holding the Alt/⌥ key and clicking on the bond. This feature works in multiselection as well holding Alt/⌥ + Shift together and clicking consecutively on bonds.
    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 drawing area to take it in hand.
    When a bond is selected in the drawing area, the top toolbar expands, enabling bond coloring.

    Coordinate bond

    The Coordinate bond can be placed in the drawing area 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 style of Coordinate bonds in the drawing area can be set from Main menu --> Settings --> Coordinate bond and the following options are available:

    • Solid
    • Hashed
    • Dashed

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

    Chain tool

    Icon Shortcut
    Chain Tool Icon Shift + x

    The Chain tool facilitates the drawing of longer chains. After taking the tool in hand click and drag in the drawing area 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 Icon Benzene a
    Cyclohexane Icon Cyclohexane 6
    Cyclopentane Icon Cyclopentane 5
    Cyclobutane Icon Cyclobutane 4
    Cyclopropane Icon Cyclopropane v
    Cyclohexane Chair1 Icon Cyclohexane chair 1 0
    Cyclohexane Chair2 Icon Cyclohexane chair 2 9
    Cycloheptane Icon Cycloheptane 7
    Cyclooctane Icon Cyclooktane 8
    Cyclopentadiene Icon 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 in the drawing area.

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

    Template library

    Icon Shortcut
    Template Library Icon Shift + i

    The Template library dialog can be opened from the left toolbar. It contains multiple structural categories with commonly used predrawn structures. Clicking on a template card closes the dialog and takes the appropriate structure into hand that can be placed on the canvas by clicking. The following categories are available by default in Marvin Pro:

    • Aromatics --> basic and condensed aromatic structures, fullerenes
    • Bicyclics --> bicyclo alkane rings
    • Conformers --> structural isomers of cycloalkanes
    • Cycloalkanes --> a set of cycloalkanes from cyclopropane to ring20
    • Hexoses --> hexoses displayed in Fischer-projection
    • Supramolecules --> crown ethers and calixarenes

    Atoms

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

    • C
    • H
    • O
    • N
    • S
    • P
    • F
    • Cl
    • Br
    • I

    Periodic Table

    Icon Shortcut
    Periodic Table Icon Shift + p

    Other atoms of the Periodic table can be selected by opening the Periodic Table dialog. In the 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 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.

    Also, it is possible to insert atoms using their shortcuts. Typing an atom label when hovering over the drawing area will take the appropriate element into hand. Typing when hovering over an atom label will exchange it automatically. If one or more atoms are selected, typing will also change their atom labels automatically. If an unavailable atom label is typed, the Abbreviated groups input field opens up. The chemical elements can also be accessed from the abbreviated groups library if the exact chemical label is added (e.g. Mg will reveal Magnesium but M will not).

    When an atom gets selected in the drawing area, 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
    RGroup Icon r

    The RGroup tool lets you place R-group labels in the drawing area 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
    Define RGroup Icon -

    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
    RGroup Attachment Icon -

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

    Variable attachment

    Icon Shortcut
    Variable Attachment Icon -

    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 group in the drawing area 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
    Charge Plus Icon Increase Charge +
    Charge Minus Icon 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.

    Shapes

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

    Icon Name
    Rectangle Icon Rectangle
    Rounded rectangle Rounded rectangle
    Ellipse Icon Ellipse
    Triangle Icon Triangle
    Star Icon Star
    Line Icon Line
    Dashed Line Icon Dashed line
    Arc Icon Arc
    Dashed arc Icon Dashed Arc

    When a shape is placed in the drawing area, 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 and its opacity can be set. Also a gray shadow can be added to the Rectangle, Rounded rectangle, Ellipse, Triangle and Star shapes.
    • Line Weight: By using this tool, the boldness of the lines can be specified in pixels.

      Holding shift during placing a Rectangle, Rounded rectangle, Triangle and Ellipse enables the creation of squares, rounded squares, equilateral triangles and circles. Also, when resizing these objects, holding shift will keep the original ratio of the shapes.
      The Star shape has fixed ratios, it cannot be distorted, only its size can be set.

    Brackets

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

    Icon Name
    Square Brackets Icon Square bracket
    Round Brackets Icon Round bracket
    Curly Bracket Icon Curly bracket

    The shortcut Shift + t will take the most recently used bracket type into hand. The Square brackets and Round brackets can be used to create S-groups.

    S-groups

    When a bracket is placed on a chemical structure, an input field pops up enabling the addition of 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 Example structures
    Link node Range of integers starting from 1 (e.g. 1-4) The bracket is placed around one atom that has two connecting and crossing bonds Link node
    Repeating unit It must have at least one range of integers* and then other ranges and positive integers are accepted (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 OR only one of the brackets has crossing bonds Repeating unit
    SRU polymer One letter of the english alphabet (e.g. n; m) The bracket is placed around a fragment with either 1-1 or 2-2 bonds crossing both brackets OR only one of the brackets has crossing bonds SRU polymer
    Multiple group Positive 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 Multiple group
    Custom bracket Any input is accepted No structural restrictions Custom group

    *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 in the drawing area 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 Arrow Icon Single
    Equilibrium Arrow Icon Equilibrium
    Unbalanced Equilibrium Arrow Icon Unbalanced equilibrium
    Rearrangement Arrow Icon Rearrangement arrow
    Resonance Arrow Icon Resonance
    Open Arrow Icon Open
    Dashed Arrow Icon Dashed
    Crossed Arrow Icon Crossed
    Hashed Arrow Icon Hashed
    Retrosynthesis Arrow Icon Retrosynthesis
    Curved Arrow Icon Curved
    Half-headed Curved Arrow Icon Half-headed curved
    Circular Arrow Icon Circular
    Single electron flow Single electron flow
    Double electron flow Double electron flow

    The type of the arrows placed in the drawing area 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 in the drawing area, the color of the object’s outline can be specified using Line Color from the top toolbar.

    Using the sohrtcut e will take the most recently used arrow type into hand. 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 in the drawing area. 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
    Monovalent radical Can host one arrow n/a
    Divalent singlet radical Can host two arrows Can host an arrow
    Divalent triplet radical Can host two arrows Can host an arrow
    Trivalent doublet radical Can host three arrows Can host an arrow
    Trivalent quartet radical Can host three 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 Icon -

    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 in the drawing area, 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
    Map reaction atoms Icon -

    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 only be created by selecting Context menu -> Radical -> Divalent singlet and adding another radical using the Add radical tool enables the creation of trivalent doublet radicals.
    If having three radicals on an atom, using the tool sets the radical state to Off, removing the unpaired electrons.

    All radical types can be set directly from the atom's context and main menu through the Radical submenu.

    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

    Icon Shortcut
    Text Icon t

    The Text tool is available from the left toolbar. Clicking in the drawing area with the Text tool in hand opens a dynamically sized text field for input. Dragging in the drawing area will create a fixed sized textbox upon release. Changes made to the text field can be saved by either clicking on an empty part of the drawing area 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 Icon Expand
    Contract Icon Contract
    Ungroup Icon Ungroup

    There are a few ways to add Abbreviated groups to the drawing area. First, hovering over an atom and starting typing results in the appearence of a dropdown menu with available abbreviated groups that can be selected by clicking on them with the cursor or pressing enter. The list is automatically filtered upon typing narrowing it down to relevant groups. Note, that chemical elements are also accessible from this library by typing exact matches. The Text tool can also be used to overwrite an atom label with an abbreviated group’s name (in this case the dropdown menu does not appear).

    Expand/Contract/Ungroup abbreviated groups

    Once an Abbreviated group is in the drawing area, it can be Expanded from its Context menu to show the underlying structure. The Expand command also cleans and selects the structure. In expanded state the attachment points of the abbreviated group are revealed offering a convenient way to create the desired chemical connections with other structures. As long as the Abbreviated group is chemically unchanged it can be Contracted from its Context menu. It is possible to attach bonds to the contracted label as they are automatically connected to the available attachment points. The connection pattern can always be revealed by expanding the abbreviated group.
    Upon modifying the chemical content of the structure (e.g. adding or removing atoms and bonds, changing the stereochemical information), the abbreviated group is automatically ungrouped and cleaned. It is possible to manually ungroup an abbreviated group from its context menu by using the Ungroup command.

    Display of abbreviated groups

    Hovering any part of the expanded abbreviated structure triggers a purple highlight feedback, indicating the structural content of the group. Also a bracket preview appears around the group displaying the label of the contracted group in the bottom right corner. The purple dots on certain atoms indicate the abbreviated group’s attachment points, where chemical structures can be attached to it. If the abbreviated group has more than one attachment point, hovering over these atoms reveal their connection index on the pointer. When connecting bonds to a contracted abbreviated group with multiple attachment points, they are used up starting with the attachment point having the index 1 followed by 2, etc. The connection pattern can be revealed by expanding or ungrouping the abbreviated group.

    Merge and split components

    Icon Name
    Merge Components Icon Merge components
    Split Components Icon 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 molecule 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 Shapes, 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, Shapes, Brackets, Arrows, Images and Scribbles.

    Mirror & Rotate

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

    When selecting chemical structures in the drawing area, 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 Icon 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. The homology groups are displayed in the drawing area with their long names. If the atom label is edited manually and the abbreviation is added, upon finishing editing the abbreviation is switched to the corresponding long name.

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

    Atom query properties can be assigned to atoms in multiselection mode as well. When there is a collision of values between atom query properties in multiselection, the dialog shows the above values. In these situations, applying a modification of the values will result in unified values on the atoms. For example, two atoms are selected, one of the having X1 and the other having X3, the dialog displays MIXED in the Connections field. Setting the value to '2' and applying the modification will result X2 on both atoms.

    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 in the drawing area 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
    Reacting center Icon Center
    Make or break Icon Make or break
    Reacting center change Icon Change
    Reacting center make and change Icon Make and change
    Reacting center not center Icon Not center

    Setting Reacting center is enabled in mixed selection as well.

    Atom properties

    When there is a selection in the drawing area 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 in the drawing area.

    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 of Radical is Off and it can be switched to the following states from the atom's context menu and if selected, from the main menu:

    • Off
    • Monovalent
    • Divalent singlet
    • Divalent triplet
    • Trivalent doublet
    • Trivalent quartet

    On the left toolbar, the Electron tool can be used to add radicals manually 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 in the drawing area. 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
    Formula&Molweight Icon Shift + c

    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 in the drawing area using the pin button. Structural changes affecting the selection will update the data content of the pinned box. If the box is pinned on a full molecule, extending the structure will also extend the selection area of the pinned box. Upon clicking the pin button again or by chemical modifications of the selected fragment, the box disappears.

    Clean

    Icon Shortcut
    Clean Icon Ctrl/⌘ + Shift + k

    Cleans the selected object. If there is no active selection, the cleaning is applied to the whole drawing area.

    Aromatize/Dearomatize

    Icon Shortcut
    Aromatize Icon Alt/⌥ + k

    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 in the drawing area, the aromatize and dearomatize method works only for the selected structure.

    Show stereo

    Icon Shortcut
    Show Stereo Icon Shift + s

    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
    Hydrogenize Icon Ctrl/⌘ + Shift + h

    Adds or removes hydrogen atoms to/from the selected structures or fragments. If there is no active selection, changes apply to every atom in the drawing area.

    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 [Ctrl/⌘ + i] 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/⌘ + i shortcut as well.

    Export

    Download as file

    Icon Name Shortcut
    Download Icon Download -
    Download as file Icon Download as file Ctrl/⌘ + s

    The Download button enables the export of the drawing area 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 file Icon Download as image

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

    Visibility settings

    In the Main menu -> Settings submenu, various visibility options are available. These settings affect the schemes in the drawing area and the imported structures as well.

    Charge

    The display of Charge may be set to Default or Circled.

    Coordinate bond

    Three display option are available for the Coordinate bonds:

    • Solid
    • Hashed
    • Dashed

    Variable attachment

    The display of the Variable attachment highlight color may be set to Color highlight or Gray highlight.

    Molecule visualization

    The display of chemical structures in the drawing area may be set from the 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

    Stereochemistry options

    The display and visibility of Molecule level and enhanced stereochemical flags can be customized in Marvin Pro. From the Stereochemistry options dialog, the visibility of molecule level stereochemical notations and atom level enhanced stereo notations can be switched between On and Off. 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 drawing area.

    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.

    Style settings

    From the Style settings dialog, the following structural display options can be set:

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

    Commonly used scientific journal styles with predefined settings are provided in the editor in a dropdown list. Currently, the following journals can be accessed from the menu:

    • ACS 1996 (default)
    • Wiley
    • Advanced Synthesis and Catalysis
    • RSC
    • Nature
    • CellPress
    • Synthesis/Synlett

    Custom styles can be defined by selecting Custom style from the predefined style list and by changing the settings. The custom styles can only be saved and applied if their settings and name differ from the existing styles. Custom styles are only persisted in the list for one user session, refreshing the page will restore the default settings of the editor and removes the saved styles.

    When there is a conflict between style settings during import, a Style options dialog pops up enabling manual resolution of the conflict. Selecting Use Imported will apply the style settings of the imported structures, while Keep Original will force the imported structure to adapt to the style settings of the drawing area.

    The effect of the modifications can be checked instantly on the dynamically changing example structure.
    The applied settings will not affect the atom fonts and/or label sizes which were set uniquely in the drawing area. *The Fixed length also scales graphical objects proportionally. Objects included are Shapes, Brackets, Arrows, Plus sign, Text boxes, Images and Scribble lines.

    CPK coloring

    CPK coloring of atoms can be switched between On and Off.

    Atom numbering

    The visibility of the Atom numbers can be set by the Enable atom numbers toggle button, affecting the whole drawing area. When turned on, all existing atom numbers are visible. Switching the toggle to Off hides the atom numbers but they are remembered by the application, thus, turning the toggle button back On will reveal them again.

    R-group attachment order

    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

    The visibility of the Valence errors can be set using the Show valence errors toggle button.

    Variable attachment highlight

    This switch icon sets the general visibility of the highlight patch of Variable attachments between On and Off.