Mouse Manual

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

[This page also in Spanish / Esta página en español : Manual Ratón ]
[This page also in French / Cette page en français : Manuel Souris ]


  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.

main button middle button secondary button
(left) (middle) (right)
Open Jmol menu Ctrl + click
or click on 'Jmol' logo
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