Viewer Modes

IQmol operates in one of four modes that change the behavior of the mouse actions. Modes are selected by clicking on the appropriate tool from the Tool Bar. In addition, some modes can be activated whilst in the manipulate mode using hot keys.

Manipulate Mode

Activating this mode changes the cursor to . This is the default mode for the viewer and allows the molecule to be rotated and zoomed.

The manipulate mode implements the following mouse functions:

  • Left click and drag: Rotate the view of the molecule. Cursor changes to
  • Middle click and drag: Zoom in and out. Cursor changes to
  • Right click and drag: Translate the view of the molecule. Cursor changes to

Build Mode

Activating this mode changes the cursor to . This mode can also be activated using the alt modifier when in manipulate mode.

The build mode implements the following mouse functions:

  • Left click: If no atoms exist, creates an atom. Clicking on an existing atom will convert it to the current build element shown in the Toolbar.
  • Click and drag: If the click originates on an atom, this will create a bond and a new atom. If the drag occurs between two existing atoms, then a bond is created (if a bond already exists then the bond order is incresed). If the click does not originate on an atom, then this action rotates the molecule as in manipulate mode.
  • Right click: Deletes any atom or bond under the cursor.

Select Mode

Activating this mode changes the cursor to . This mode can also be activated using the shift key when in manipulate mode.

The select mode implements the following mouse functions:

  • Left click: Adds atom or bond to selection.
  • Click and drag: Creates a selection rectangle, all atoms and bonds within the selection rectangle are added to the selection.
  • Right click: Removes atom or bond from selection.

If the following items are selected, appropriate geometric infomation is displayed in the bottom left of the viewer window:

  • Atom: Element type
  • Bond: Bond length
  • Two atoms: Inter-atomic distance
  • Three atoms: Bond angle
  • Four atoms: Torsion angle

The selected geometric parameter can be constrained using the menu option Build→Fix Constraint. This will fix the value of this parameter when the button is pressed.

Manipulate Selection Mode

Activating this mode changes the cursor to . This mode manipulates only the selected atoms, and can only be activaed using the ctrl modifier (⌘ key on Mac). This mode is useful for moving and orienting separate fragments in the molecule.

The manipulate selection mode implements the following mouse functions:

  • Left click and drag: Rotate the selected atoms about their center. Cursor changes to
  • Right click and drag: Translate the selected atoms. Cursor changes to