Command Short Cuts

Using the mouse:

Command-Click:              Select a rotation atom

Command-DoubleClick:   Select/Deselect a torsion atom

Option-Click:                  Select/Deselect atom

Option-DoubleClick:      Display atom info

Control-Click:                 Select/Deselect block

Control-DoubleClick:     Display block info
(the rotation and torsion atoms are marked in red)
To (un)mark all blocks: Control-Option.
To deselect a torsion atom: Command-DoubleClick far from any atom.
To deselect all selected atoms: Option-Click far from any atom.
To deselect all selected blocks: Control-Click far from any atom.

Clicking and dragging the mouse under the dashed line drawn in the bottom part of the Image window will provide some handy structure manipulation features:
• Rotation around the selected rotation axis (usually Z-axis).
• With the ControlKey down: Zooming in and out. If this operation is performed with the ShiftKey down, the zoom factor will remained unchanged while the visible surrounding of the rotation atom will be changed instead.
• With the ShiftKey down (a torsion atom must have been previously selected): Turning the torsion bond clockwise and counter clockwise. If this operation is performed with the OptionKey down, the display mode will be changed in order to make the atom clashes visible.

Using the keyboard:
⌘O
:
Open a structure file (one at a time). OptionKey opens a portion of the structure. ControlKey opens a second structure.
⌘Z, ⌘X, ⌘C, ⌘V
: Usual edit short cuts.
⌘R and ⌘L
:
Rotate Right and Left OR with the mouse dragged BELOW the dashed line drawn at the bottom part of the image window.
⌘W
:
Wobble.
⌘T
:
Tumble.
⌘F
:
Simulate Folding (automatic). OptionKey returns control to the user. ShiftKey report structural information concerning each residue.
⌘+ and ⌘-
:
Zoom In and Out OR with the mouse dragged BELOW the dashed line drawn at the bottom part of the image window with the ControlKey down. The surround visibility (not the zoom factor) is modified when the ShiftKey is down.
⌘* and ⌘/
:
Turn bond clockwise and counterclockwise around the torsion atom OR with the mouse dragged BELOW the dashed line drawn at the bottom part of the image window with the ShiftKey down. To turn a bond, a torsion atom must have been previously selected (⌘ DoubleClick on an atom).
⌘A
: Add a block at the end of a structure of the same type as the last one.
⌘U
: Undo the last block of a structure.
⌘B
:
Swap rotation axis (ShiftKey reverses the order).
⌘M
:
Swap display mode (ShiftKey reverses the order).
⌘H
:
Show/Hide Hydrogen-bonds.
⌘I
:
Show/Hide Ionic-bonds.
⌘S
:
Stereo display.
⌘?
:
Write structure file header or residue composition of frontmost utility window.
⌘,
:
Open Utilities/Visibility... dialog.
⌘;
:
Open Utilities/General Selection... dialog.
⌘:
:
Open Utilities/Specific Selection... dialog.
⌘=
:
Move structure to place the rotation atom at the image window center. OptionKey fits structure to image window.
⌘2
:
Motion only the second structure (when 2 structures have been loaded into memory).

Additional Short Cuts

⌘¨, ⌘Æ ⌘≠ and ⌘Ø are used to change some parameters dynamically.
The action depends on the kind of the FrontMost Window: 

Image window (stereo mode):

⌘¨ and ⌘Æ act on the value of the Stereo Angle.

Image window (if it contains an ED-map):

⌘≠ and ⌘Ø act on the value of the Lower Threshold of the ED-map.

TopW and ClashW windows:

⌘≠ and ⌘Ø act on the value of the Profile Energy Maximum.

AroundW & MotivW windows: 

⌘≠ and ⌘Ø act on the value of the Histogram Ordinate Maximum.

⌘≠ and ⌘Ø act on the value of the Significative Level if preference values are displayed.

StatW windows: 

⌘≠ and ⌘Ø act on the value of the Histogram Ordinate Maximum.

⌘¨ and ⌘Æ act on the value of the Histogram Sampling Width.

StructW windows: 

⌘≠ and ⌘Ø act on the value of the Histogram Ordinate Maximum.

⌘≠ and ⌘Ø act on the value of the Significative Level if preference values are displayed.

TabKey cycles through the windows of the same kind (ShiftKey reverses the order).
Hitting the keyboard 'Help' key toggles the FoldIt Balloon Help.