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.
To insert a IUPAC Name choose it from the Insert menu, it will be automatically inserted under the structure. The name will be updated real-time.

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

Templates can be rotated into the desired position
- after putting, by moving the pointer while the mouse button is down,
- or before the structure is picked up:
  1. Move the mouse pointer over the template template button.
  2. Press the mouse button when you find the desired position.
Joining a structure with a template (click here for pictures).
- Simplest case
  1. Select the template.
  2. Move it near the structure. Attaching points are signed by circles.
  3. Click.
- You can rotate the template if there is only one main attaching point.
  1. Select the template.
  2. Move it near the structure. The main attaching point(s) are the big circle(s).
  3. If there is only one main attaching point, press and hold the mouse button.
  4. Rotate the template into the desired position by moving the mouse.
To choose from another template set in MarvinSketch: select from the Insert/Templates menu

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

All the elements. For example: N is Nitrogen, Cl is Chlorine etc. (Also works in lower case: n, cl etc.)
Query atom types: * (any atom), Q (heteroatom), R-groups: R1, ..., R32767. (Also in lower case.)
Atom maps for reactions: M1, M2, ..., M+ (next unused mapping number), Unmap: M0. (Also in lower case.)
Bond types: 1, 2, 3, 4 (aromatic), 1-2 (single or double), 1-4 (single or aromatic), 2-4 (double or aromatic), 0 (any)
Charges: -, +
Stereochemical groups: abs (ABSOLUTE), or1, or2, ..., or10, ... (OR n), and1, and2, ..., and10, ..., &1, &2, ..., &10, ... (AND n)
Abbreviated groups: Ph = Phenyl, Ala = Alanyl, etc. (Also in lower case.)
To complete a longer name, press Enter or End after typing the first few characters.
Templates: 1-1, 2-2, ... 9-9
Special atom properties: .a (aromatic), .A (aliphatic), .u (unsaturated), .H0, .H1, ... (number of hydrogens), .h0, .h1, ... (implicit hydrogens), .X0, .X1, ... (connectivity), .D0, .D1, ... (degree), .R0, .R1, ... (rings), .r3, .r4, ... (smallest ring size), .s*, .s0, .s1, ... (substitution count), .v0, .v1, ... (valence), .rb*, .rb0, .rb1, ... (ring bond count).
More window (Periodic Table): Ctrl-M
Undo: Ctrl-Z, Alt-Backspace, Redo: Ctrl-Y
Clipboard. Copy: Ctrl-C, Copy as Smiles: Ctrl-L, Cut: Ctrl-X, Paste: Ctrl-V, Select all: Ctrl-A
File operations (if available). Open: Ctrl-O, Save: Ctrl-S, Print: Ctrl-P
To define a set of fragments as R-group 5: select the fragments, then type R-5.
To choose an attachment point on R-group 5: type R-5, then click on the atom.

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