MarvinSketch Quick Help

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,
    • when the C button is down, by moving the pointer while the mouse button is pressed.
  • To select another bond type, press the Bond button and hold the mouse button down 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
Selecting
  • 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 selection, press and hold down Shift while selecting.
  • To decrease selection, press Shift while clicking a selected 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.
  • Use the R1, ..., R32 buttons for R-group operations.
  • Use the Groups menu to select an abbreviated group.
Graphic 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, Rotating, Zooming
  • View transform modes:
    • F5 - none (back to sketching)
    • F6 - Zoom mode:
      Hold down mouse button while dragging mouse vertically to zoom.
    • F7 - Rotate in 3D mode
    • F8 - Zoom/Rotate mode:
      Hold down mouse button while dragging mouse vertically (to zoom) or horizontally (to rotate).
  • To move the selection,
    1. press Shift once,
      (alternatively: move 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. press Shift twice,
      (alternatively: move mouse pointer towards the "edge" until a blue gear appears)
    2. drag the selection by pressing and holding down the mouse button.
  • To rotate the selection in 3D,
    1. press Shift 3 times, then
    2. drag the selection by pressing and holding down the mouse button.
  • To move an atom, drag it with the mouse in Select mode.
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
Note: 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.
Use the Edit menu to
  • undo, redo, copy, cut, paste or select all,
  • clean in 2D or 3D,
  • flip or mirror horizontally or vertically,
  • (de)aromatize,
  • add/remove Hydrogen atoms, atom maps, data,
  • create, contract, expand or ungroup S-groups,
  • set R-group query conditions,
  • specify the chiral flag,
  • view or edit the Source (Molfile, SMILES string, etc.),
  • edit Preferences.
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).
Template structures Reactions
  • To create a reaction:
    1. Press the arrow button.
    2. Draw an arrow from reactants to products.
  • To map reaction manually:
    1. Press the arrow button.
    2. Draw an arrow from a reactant atom to the corresponding product atom.
    alternatively:
    1. Press m# where # is the map number to add (for example m1).
    2. Click on an atom to assign the map.
  • To map reaction automatically:
    1. Select some atoms to map.
    2. Press the Edit/Atom Mapping/Auto Map menu item.
  • To remove maps:
    1. Select atoms to remove their maps.
    2. Press the Edit/Atom Mapping/Clear Map menu item.
    alternatively:
    1. Select atoms to remove their maps.
    2. Press m0.
R-groups
  • To define a set of fragments as R-group 5,
    1. select the fragments,
    2. type R-5 or press R5 in the More window.
  • To set query conditions, use Edit / Attributes / R-logic
  • To choose an attachment point on R-group 5,
    1. type R-5 or press R5 in the More window,
    2. click on the atom.
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