Draw Chemical Structures in Marvin JS

Add an atom of one of the following elements: H, C, N, O, S, F, P, Cl, Br, I

1. Click the element symbol.
2. Click in the drawing area.

Add any atom

1. Click .
2. Click the element symbol in the periodic table.
3. Click in the drawing area.

Add an atom list or not list

1. Click .
2. Click either Atom List or NOT list.
3. Click the element symbols to be listed.
4. Click OK.
5. Click in the drawing area.

Add an atom and its bond to an existing atom

1. Click the element symbol for the new atom.
2. In the drawing, drag from the existing atom away until the symbol for the new atom is displayed under the pointer.

Add two bonded carbon atoms

1. Click and hold the bond button to expand it.

   This button displays the last selected bond type — by default, .

2. Click .
3. Click in the drawing area.

Add a chain of carbon atoms

1. Click .
2. In the drawing, drag until the number of carbon atoms you want to insert is displayed under the pointer.

Some modes: Add an R-group

1. Click .
2. Click in the drawing area.

Replace an atom

1. Click the element symbol for the new atom.
2. Click the atom to be replaced.

Change an Atom

1. Right-click an atom in the drawing and click Atom properties.
2. For Change to, select Query or R-group.
3. Query atoms: Type the label in Atom.
4. R-groups: For R, click and then type the R number.
5. Click OK.

Add a bond between existing atoms

1. Click and hold the bond button to expand it.

   This button displays the last selected bond type — by default, .

2. Click the bond type you want to use.
3. In the drawing, drag from one atom to another.

Change a bond type or direction

1. Click and hold the bond button to expand it.

   This button displays the last selected bond type — by default, .

2. Click the bond type you want to use.
3. Click the bond to be changed.

Increase or decrease an atom's charge

1. Click or .
2. Click an atom. Click until the correct charge is shown.

Some modes: Add radicals or lone pairs to an atom

1. Click and hold the radical / lone pairs button to expand it.

   This button displays the last selected item — by default, .

2. Click either or .
3. Click an atom. Click until the correct number of radicals or lone pairs is shown.

Some modes: Draw a curved harpoon to show the movement of electrons

1. Click and hold the electron flow button to expand it.

   This button displays the last selected electron flow arrow — by default, .

2. Click either or .

3. Drag from the source electrons (or bond) to the target atom.

   The electron flow arrow points to an incipient bond between the atoms.

4. Click the electron flow arrow to toggle its target between the incipient bond and the target atom.

aromatized ring

or

Your students can draw a clockwise, counterclockwise, or aromatized ring in the answer and be marked correct.

double cis or trans bonds

or

Your students can draw either cis- or trans-configuration around the double bond and be marked correct.

single up or down bonds

single up or down bond

Your students can draw either a single up or a single down bond and be marked correct.

Some modes: Add a reaction arrow

1. Click and hold the reaction arrow button to expand it.

   This button displays the last selected reaction arrow type — by default, .

2. Click the reaction arrow you want to use.
3. In the drawing, drag the pointer in the direction the arrow should point.

Some modes: Add a + sign in a reaction

1. Click the reaction arrow button.
2. Click in the drawing area.

When adding a + sign, it does not matter what kind of reaction arrow is selected.

Some modes: Add agent names to a reaction arrow

In WebAssign Marvin JS questions, use psuedo-atoms to specify agent names above reaction arrows.

1. Click and hold the query atom button to expand it.

   This button displays the last selected query atom — by default, A.

2. Click ?.

3. Type the label for your pseudo-atom and click OK.

   Subscripts are automatically formatted. For example, type H2O to display H2O.

4. Click in the drawing area.

Set a mapping number for an atom

1. Right-click an atom in the drawing and click Atom properties.
2. For Map, click and then type the mapping number.
3. Click OK.

Select a single item

1. Click either or .
2. Click an item to select it.

Select an entire structure

1. Click either or .
2. Double-click any part of a structure to select the entire structure.

Select multiple items

1. Click either or .
2. Click an item to select it.
3. Hold the SHIFT key and click additional items.

Select items in a rectangular region

1. Click and hold the selection button to expand it.

   This button displays the last selected selection type — by default, .

2. Click .
3. In the drawing, drag to select items.

Select items in an arbitrary region

1. Click and hold the selection button to expand it.

   This button displays the last selected selection type — by default, .

2. Click .
3. In the drawing, draw a boundary to select items.

Cut, copy, paste

Click , , or .

Delete items

Either:

• Select items and then click .
• Click and then click items to delete them.

Move an item or selected items

1. Click either or .
2. If needed, select multiple items to move together.
3. Move the pointer over part of a selected item and drag it to a new location in the drawing.

Rotate items in 2 dimensions

1. Click either or .

2. Select one or more items to rotate.

   A rotation handle is displayed whenever the selection can be rotated.

   

3. Drag the rotation handle to rotate the selection around its center.

Standardize bond lengths and angles (2-dimensional)

Click .

This improves the appearance of your drawing and converts it to 2-dimensional if needed.

Some modes: Standardize bond lengths and angles (3-dimensional)

Click .

This improves the appearance of your drawing and converts it to 3-dimensional if needed.

Undo your last change

Click or press CTRL+Z.

Clear the drawing area

Click .

Zoom in or out

1. Click and hold the zoom button to expand it.

   This button displays the last selected zoom type — by default, .

2. Click or .
3. Click the button again to zoom more.

Zoom to drawing

1. Click and hold the zoom button to expand it.

   This button displays the last selected zoom type — by default, .

2. Click .

Zoom to selection

1. Select one or more items in the drawing.

2. Click and hold the zoom button to expand it.

   This button displays the last selected zoom type — by default, .

3. Click .

Some modes: Rotate drawing in 3 dimensions

1. Click .

2. Drag in the drawing area to rotate the drawing.

   Hold the SHIFT key to constrain rotation to either the x or y axis.