ChemAxon Ltd MarvinSketch
How to draw
  • Carbon atoms connected by single bonds can be drawn when the Bond button is down and its icon shows a single bond.
  • To select another bond type, hold the mouse button down on the icon until a menu pops up.
  • To change a single bond to double (triple), select single bond mode, then click on the bond once (twice).
  • To change an atom, press an atom button such as B, N, O, F, etc. and then click on the atom.
  • To increase or decrease a charge, select + or - and click on the atom.
  • Red underline means valence error.
Undo and Redo
  • Operations can be reverted with Undo and Redo.
How to delete
  • To delete the selection, press Erase.
  • To delete atoms or bonds one by one,
    1. be sure there is no selection,
    2. press Erase,
    3. click on the atoms/bonds
  • To delete everything in a rectangle,
    1. press Erase,
    2. press and hold down the mouse button while selecting the rectangle
    3. release the button
  • To delete a nonrectangular area,
    1. press Erase,
    2. click on the mouse button and move the mouse pointer around the fragment
    3. click again
  • Press the Select button.
  • To select an atom, bond or group, click on it.
  • To select a fragment, double click on an atom or bond of it.
  • Lasso selection: Click on the mouse button and move the mouse pointer around the fragment. Click again when you are ready.
  • Rectangle selection: Hold the mouse button down while selecting.
  • To increase or decrease selection, press Shift while clicking on an atom, bond or group.
  • To unselect all the atoms, click on the sketchboard somewhere outside the structure.
The More window
  • Press More to bring up a window with a periodic table, query atoms, the SMARTS/Alias textfield and a menu of abbreviated group,
  • To choose a SMARTS query atom or property not found in the left button bar,
    1. write its SMARTS string into the textfield,
    2. press SMARTS.
  • To define a set of fragments as R-group 5,
    1. select the fragments,
    2. press R5.
  • To choose an attachment point on R-group 5,
    1. press R5,
    2. click on the atom.
  • To select an abbreviated group, use the Groups menu.
Graphics objects and text boxes
  • To insert a (poly)line, rectangle or text box, choose it from the Insert menu, point with the mouse to the desired position, then click or drag. After putting a text box, you can immediately use the keyboard to type a text.
  • To change the contents of a text box, choose Select mode, click on the box, then use the keyboard.
  • To resize or change the shape of an object, drag one of its points.
Moving and Rotating
  • To move an atom, drag it with the mouse in Select mode.
  • To move the selection,
    1. move the mouse pointer towards the center until a blue rectangle appears,
    2. drag the selection by pressing and holding down the mouse button.
  • To rotate the selection,
    1. move the mouse pointer towards the "edge" until a blue gear appears,
    2. drag the selection by pressing and holding down the mouse button.
Drag & Drop
  • Selections can be moved also between different Marvin windows
  • Molecule files from the file manager or the desktop can be dragged and dropped in Marvin
1. D&D only works in the Swing version, in Java 1.2 or later.
2. D&D does not work in the JMSketch applet running in a browser window, because drop events are received by the browser in that case.

Hydrogen labels

  • In the View menu, choose Hydrogens to change the way implicit H labels are shown.
If you do not see View and Edit menus, put the sketcher into a separate window by pressing the top left button (an arrow pointing up).

Use the Edit menu to

  • copy or paste,
  • clean in 2D or 3D,
  • aromatize or dearomatize,
  • add or remove Hydrogen atoms,
  • flip horizontally or vertically,
  • specify the chiral flag
  • set R-group query conditions
  • view or edit the Source
    (Molfile, SMILES string, etc.)
Template structures Reactions
  • To select reactants and products,
    1. press the arrow button,
    2. draw an arrow from reactant to product.
  • To map atoms,
    1. press the arrow button,
    2. draw an arrow from an atom in the reactant to the same atom in the product.
Keyboard shortcuts Right click on an atom, bond or group for a pop-up menu to
  • set ion charge
  • set radical value
  • set atomic weight (for isotopes)
  • set atom map
  • set R-group label
  • set bond type
  • set bond query attributes:
    - cis/trans stereo care box
    (double bond stereo information is ignored if Stereo search is unchecked)
    - topology: ring or chain
  • align horizontally or vertically
  • contract group
  • expand group
  • ungroup