Mouse Manual

Jmol / JSmol Tutorials

A list of Jmol / JSmol Tutorials written by users.
Using the mouse (English · Español · Français · Japanese).
Scripting quickstart: rendering options · selecting atoms.
How to create surfaces and isosurfaces, including cavities, pockets and tunnels.
Displaying shapes, polyhedra, orbitals, dipoles, distances, forces and vibrations.
Creating movies.
Customizing Jmol: macros · menus.
Web pages without writing code by using the Jmol "Export to Web" function.

	Reference: English – Other: Español · Français · 日本語 ·

Manual for manipulating the molecules using the mouse in Jmol (also called 'mouse gestures')

Notes:

In the usual configuration, "main button" is the left button, and "secondary button" is the right button.
Reportedly, on single-button mice Alt drag may be equivalent to drag with middle button.

	main button	middle button	secondary button
	(left)	(middle)	(right)

Open Jmol menu	Ctrl click or click on 'Jmol' logo		click

Rotate around X,Y	drag

Move along X,Y (= translate)	Shift double-click and drag	double-click and drag	Ctrl drag
	works both when clicking on the molecule or away from it

Reset and centre	Shift double-click*	double-click*
	*only works if double-click is done away from the molecule

Rotate around Z	Shift drag horizontally	drag horizontally	Shift drag horizontally (possibly fails in Mac's)

Zoom in / out	Shift drag vertically	drag vertically
	or use mouse wheel

	Implemented only on Jmol 10.00.22 prerelease and later: Only work after a `slab on` command has been issued
Slab (slab from front)	Ctrl Shift drag (vertically) *
Depth (slab from back)	Ctrl Shift double-click and drag (vertically) *
Shift the slab (change slab and depth maintaining constant thickness)	Alt Ctrl Shift drag (vertically) *
	*if this fails on a Mac, try pressing the mouse button first, then the Ctrl Shift keys, then drag
	Slab can be tested in this page

set picking group

to toggle selection for an entire amino acid by clicking on one of its atoms,

set display selected

is set to monitor the selection status.

Distance (2 atoms):
1. double-click on the starting atom
2. to fix a distance measurement, double-click on second atom
Angle (3 atoms):
1. double-click on the starting atom
2. click on the second atom (central atom in angle)
3. to fix an angle measurement, double-click on third atom
Torsion angle or dihedral (4 atoms)
1. double-click on the starting atom
2. click on the second atom
3. click on the third atom
4. to fix a dihedral angle measurement, double-click on fourth atom
In all cases:
- move pointer over destination atom in order to see measurement results without leaving a permanent measurement
- move outside the window in order to cancel the measurement
- make the same measurement again in order to delete the measurement