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.

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

How to change atom coordinates

This section describes how to move individual atoms within a model with the mouse.

Transformations like rotations or translations are normally applied to all atoms identically. And the stored coordinates of the atoms are not changed. But Jmol can also be configured to move some atoms individually and store the changed coordinates permanently.

There are two modes available:

1. Moving only whole molecules, e.g. a whole chain
2. Moving atoms independent of their connectivity

This section concentrates on the second mode. The two following settings are needed to activate it:

1. set allowMoveAtoms on;
2. set allowRotateSelected on;

There are additional switches available that influence what can be done and how it can be done:

1. set picking
2. set pickingStyle
3. set dragSelected

The table below summarizes information for three of the possible setting combinations (tested in Jmol 14.3.13).

	Basic options: set allowMoveAtoms on; set allowRotateSelected on;
	Option Set 1: set picking dragSelected; set pickingStyle select toggle; set dragSelected off;			Option Set 2: set picking dragSelected; set pickingStyle select drag; set dragSelected off;			Option Set 3: set picking atom; set pickingStyle select toggle; set dragSelected on;
	Click Type	Click Target	Comment	Click Type	Click Target	Comment	Click Type	Click Target	Comment
Atom Movement (only selected atoms)
x/y-shift (along screen axes)	drag	any atom		drag	any atom		shift-alt-drag	anywhere
z-shift (perpendicular to screen)	shift-drag	any atom				not available			not available
rotate	alt-drag	any atom				not available	alt-drag	anywhere
Atom Selection
select a single atom			not available	shift-drag	around an unselected atom		click	an unselected atom
				alt-drag	around an atom		double-click	an atom	other atoms are deselected
deselect a single atom			not available	shift-drag	around a selected atom		click	a selected atom
select multiple atoms			not available	shift-drag	around unselected atoms				not available
				alt-drag	around atoms
deselect multiple atoms			not available	shift-drag	around selected atoms				not available
Summary
	Option set 1 (+ basic options) totally disables mouse-based selection changes and enables all three movement types (x/y-shift, z-shift, rotate).			Option set 2 (+ basic options) enables mouse-based single/multiple atom selection changes and enables only one movement type (x/y-shift).			Option set 3 (+ basic options) enables mouse-based single atom selection changes and enables two movement types (x/y-shift, rotate).

Contributors

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