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.

To toggle the selection status of individula atoms:
Using the menus:

1. Jmol->Main Menu->Select->Selection Halos (This is optional but very helpful. It shows you which atoms are selected by plaing a golden ring around it.)
2. Jmol->Main Menu->Select->None (Needed because "select all" is the default at load time. Notice the non-zero number in parenthesis after the word select in the main menu. That is the number of items currently selected.
3. Jmol->Main Menu->Set picking->Select Atom

Now click an atom once to select, click again to deselect. The halos let me know the current selection state of each atom and the count in parenthesis after the Select in Jmol->Main Menu gives me a count of the number of atoms selected. Cipto Junaedy, cipto junaedy

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