Tools Overview

    This page briefly describes all Marvin Pro tools. You can use it as a quick reference guide or as a baseline to check whether Marvin Pro fulfills all your editing requirements.

    The tools in this document are separated into the following categories:

    General Tools

    Selection

    Icon Shortcut
    Selection Icon If another tool is selected, pressing Esc changes the active tool back to selection. Ctrl+A selects all objects on the canvas.

    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 for whole structure selection.

    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.

    The selection tool mode affects the behavior of other tools, for example, with lasso selection, the deletion and painting of structures also become lasso-like.

    Erase

    Icon Shortcut
    Selection Icon Delete or Backspace

    If you press it while not hovering over an object, it makes erase the active tool, otherwise, it deletes the object. Can be used for both single (click) and multiple (drag) deletions.

    Undo-Redo

    Icon Shortcut
    Undo IconRedo Icon Ctrl+Z and Ctrl+Y

    Undo: Revokes the last editing step.

    Redo: This 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 zoom value is 10% and the maximum is 500%.

    Additionally, you can use the shortcut mentioned above to zoom in or out. Plus and minus buttons are also available from the zoom drop-down menu. You can use the two additional zoom actions from this menu, too: Fit to Canvas and Fit to Selection.

    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.

    Open

    Files can be opened through Menu > Open or by using the Ctrl+O shortcut. The open action overwrites the contents of the canvas.

    Insert

    Contents of a file can be appended to the canvas through Menu > Insert or by using the Ctrl+I shortcut. The insert action does not overwrite the contents of the canvas.

    Copy

    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 following additional formats are available under Copy as other format:

    • MDL Molfile
    • SMILES
    • InChI
    • InChIKey
    • MDL Molfile V3000
    • PNG

    Download

    Icon Shortcut
    Download Icon N/A

    It is possible to download Marvin Pro drawings both as chemical files and images.

    The Download as image button opens a dialog in which the image format, width, and height can be set. Marvin Pro supports the following image file formats:

    • PNG
    • JPG
    • SVG
    • WebP

    The Download as file button opens a dialog in which the chemical file format can be specified. Marvin Pro supports the following chemical file formats:

    • MRV
    • MDL Molfile
    • CXON
    • SMILES
    • InChI
    • InChIKey
    • MDL Molfile V3000
    • CDX File format
    • SKC File format

    For more information about file formats, see File Formats

    Images and files can also be downloaded through Menu > Download > Image and Menu > Download > File, respectively.

    Chemical Tools

    Bonds

    All bonds that are available from this tool’s combo box are listed below.

    For a list of shortcuts, see Shortcuts.

    Icon Name
    Single Bond Icon Single Bond
    Double Bond Icon Double Bond
    Triple Bond Icon Triple Bond
    Up Wedge Bond Icon Up Wedge Bond
    Down Wedge Bond Icon Down Wedge Bond
    Wavy Bond Icon Wavy Bond
    Hashed Bond Icon Hashed Bond
    Dashed Bond Icon Dashed Bond
    Bold Bond Icon Bold Bond
    Single or Double Bond Icon Single or Double Bond
    Single or Aromatic Bond Icon Single or Aromatic Bond
    Double or Aromatic Bond Icon Double or Aromatic Bond
    Any Bond Icon Any Bonds

    When a bond is selected, a new tool called Line Color appears on the top toolbar. By using this tool, any bond can be colored one of the predefined colors.

    Chain

    Icon Shortcut
    Chain Tool Icon N/A

    A click with this tool places a single bond on the canvas. Dragging with this tool creates a chain. The number of carbon atoms is displayed next to the cursor.

    Templates

    All templates that are available from this tool’s combo box are listed below.

    For a list of shortcuts, see Shortcuts.

    Icon Name
    Cyclohexane Icon Cyclohexane
    Cyclopentane Icon Cyclopentane
    Cyclobutane Icon Cyclobutane
    Cyclopropane Icon Cyclopropane
    Benzene Icon Benzene
    Cyclohexane Chair1 Icon Cyclohexane Chair1
    Cyclohexane Chair2 Icon Cyclohexane Chair2
    Cycloheptane Icon Cycloheptane
    Cyclooctane Icon Cyclooctane
    Cyclopentadiene Icon Cyclopentadiene

    Atoms

    The following atoms are readily available from the combo box:

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

    Other atoms can be selected by clicking the Periodic Table button. When an atom gets selected, the following new options appear on the top toolbar:

    • Font Type
    • Font Size
    • Bold
    • Italic
    • Underline
    • Text Color
    • Superscript
    • Subscript
    • Formula

    RGroup

    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.

    Define RGroup

    Icon Shortcut
    Define RGroup Icon N/A

    Selecting with the Define RGroup tool creates a definition with the selected fragments and assigns an R-group label to it. Similarly to the RGroup tool, the numbering starts with R1, then the number is automatically increased. Marvin Pro also checks the canvas for R-group labels without a definition and matches the numbering accordingly. By using the Text tool, the labels can be rewritten.

    Query Atoms

    All query atoms that are available from this tool’s combo box are listed below.

    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

    Charge

    Icon Shortcut
    Charge Plus IconCharge Minus Icon + and - respectively. Only usable when the context is an atom.

    The charge can be also set from an atom’s context menu. Simply right-click the atom and select from the predefined values (2+...2-) or specify a custom value by clicking the three dots.

    Formula & Molweight

    Calculates the Formula and Mass of selected structures or fragments. The calculation automatically updates while dragging the cursor during selection.

    Clean

    Icon Shortcut
    Clean Icon N/A

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

    Aromatize/dearomatize

    Icon Shortcut
    Aromatize Icon N/A

    Aromatize: Transforms the molecule from Kekulé representation to aromatic representation by using the general aromatization method.

    Dearomatize: 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 work only for the selected structure part.

    Show Stereo

    Icon Shortcut
    Show Stereo Icon N/A

    Assigns the R or S label to a chiral center and the E or Z label to an unsymmetrical double bond.

    Name to Structure

    A free text field for importing structures based on their names. IUPAC and the traditional names of chemicals are supported.

    For more information about the underlying technology, see Name to Structure.

    Graphical and Textual Tools

    Borders and Lines

    The table below lists the tools available from this combo box.

    Icon Name
    Rectangular Border Icon Rectangular Border
    Ellipse Icon Ellipse
    Line Icon Line
    Dashed Line Icon Dashed Line

    When a rectangular border or an ellipse gets selected, 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 specified.
    • Line Weight: By using this tool, the boldness of the lines can be specified in pixels.

    Square Brackets

    Icon Shortcut
    Square Brackets Icon N/A

    When a square bracket is selected, its line color can be changed by using the Line Color tool.

    Arrows

    The table below lists the tools available from this combo box.

    Icon Name
    Single Arrow Icon Single Arrow
    Resonance Arrow Icon Resonance Arrow
    Open Arrow Icon Open Arrow
    Dashed Arrow Icon Dashed Arrow
    Crossed Arrow Icon Crossed Arrow
    Hashed Arrow Icon Hashed Arrow
    Curved Arrow Icon Curved Arrow
    Half-headed Curved Arrow Icon Half-headed Curved Arrow
    Circular Arrow Icon Circular Arrow

    Arrows can be colored by using the Line Color tool that appears on the top toolbar after selecting an arrow.

    Plus Sign

    Icon Shortcut
    Plus Sign Icon N/A

    The plus sign is a graphical object that can be used in reaction drawings, for example.

    Text

    Icon Shortcut
    Text Icon N/A

    Clicking the canvas with this tool opens a free text field for textual input. Changes made to this field can be saved by either clicking the canvas or hitting Esc. Enter can be used for inserting line breaks. When a text field is being edited, the following options appear on the top toolbar:

    • Font Type
    • Font Size
    • Bold
    • Italic
    • Underline
    • Superscript
    • Subscript
    • Formula
    • Symbols
    • Text Color
    • Highlight Color
    • Align Left
    • Align Center
    • Align Right

    Isotopes

    By using the Text tool, isotopes can be added to atoms. Just type the desired isotope number before the atom label.

    Image

    Icon Shortcut
    Image Icon N/A

    Clicking this 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.

    Paint

    Icon Shortcut
    Paint Icon N/A

    With this tool, you can change the color of an object (clicking) or every canvas object at once (dragging). Images are excluded. The main difference between this tool and the other, more specific coloring tools is that Paint allows you to color formulas as well.

    Scribble Tool

    Icon Shortcut
    Scribble Icon N/A

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

    The scribble can be selected, dragged, rotated, and resized. It is also possible to change its color either with the Paint tool or with the Line Color tool.

    Document Settings

    • Menu > Document Settings > Charge > Circled: Appends a small circle around the charges.
    • Menu > Document Settings > Default copy format: Controls the format in which the structures are copied to the clipboard. The available options are as follows:
      • CXON (Default option)
      • MRV
    • Menu > Document Settings > Molecule visualization: Opens the Molecule visualization menu where the following atom visibility settings can be set:
      • No implicit hydrogens
      • Skeletal (Default option)
      • Implicit hydrogens on terminals and heteroatoms
      • Heavy atoms without implicit hydrogens
      • Structural
    • Menu > Document Settings > Show enhanced stereochemistry: Enables enhanced stereochemistry visibility. Once the visibility is turned on, you can change the abs enhanced stereo labels to and or or labels from an atom's context menu. Please note that, these context menu items are still visible when this setting turned off, but they are grayed out and inactive.