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.

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

Notes:

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

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	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

How to select

• Use the appropriate picking command, e.g.

set picking group

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

• Click on an atom will toggle selection status.
• Most useful while

set display selected

is set to monitor the selection status.

How to make measurements

• 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

Contributors

Hansonr, Rhuehne, AngelHerraez, Ted, Pimpim, Cudo29, NicolasVervelle, Tania, Domtheo