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Shortcut Keys

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Rather than navigate the menus at the bottom of the screen to perform tasks, it is generally faster and easier to use shortcut keys (sometimes along with cursor movement or clicking). The following is a list of shortcuts that may help improve your experience:

[Click here for a single-page printable cheat sheet]

Best view Edit

  • Q key (and Home on Win OS): re-center the protein on your screen — useful if you have lost your protein off-screen
  • Click and drag (background): rotate the protein to see the other faces (without changing the shape)
  • Right click and drag (background): move the entire protein (without changing the shape)
  • Scroll of the mouse / shift click and drag / middle click and drag: zoom in and out


Original Interface
Actions affect all unfrozen elements of the protein

Selection Interface
Actions affect all unfrozen elements of the selected segments, or the entire protein if no segments are selected

W Global wiggle backbone and sidechains
E Wiggle sidechains only
T Wiggle backbone only
Y Wiggle backbone only Mutate sidechains
M Mutate sidechains
S Shake sidechains
! Idealize
left-click+drag Nudge see Bands
space bar Stops any ongoing action, in realtime — preserving the instantaneous score

Bands Edit

Original Interface Selection Interface
left-click+drag segment Create a rubber band
shift-click+drag segment Create a rubber band
shift-alt-click+drag segment Create a rubber band without snapping to any protein elements
D Disable or enable all rubber bands
R Remove all rubber bands
click midband Delete rubber band
click band end Center band end at clicked point
left-click+drag band end Move band end to a new location
alt-click+drag band end Move band end to a new location without snapping to any protein elements

Freezing Edit

Original Interface Selection Interface
F Freeze the entire protein / unfreeze all frozen elements
shift-click / middle-click Freeze element (segment or sidechain)
shift-double-click Freeze entire structure (backbone only)
left-click Freeze element (segment or sidechain)
left-double-click Freeze entire structure (backbone only)


  • Z or ctrl-Z: undo
  • Shift-Z or ctrl-Y: redo
  • Ctrl-B: restore best
  • Ctrl-shift-N: set recent best
  • Ctrl-N: restore recent best
  • A: in original interface, restore absolute best
  • I: in original interface, restore credit best
  • Ctrl-R: prompt a puzzle reset — not automatic, so reset can still be cancelled
  • Ctrl-E: reset structure
  • Ctrl-P : return to puzzle menu; switch puzzle
  • Ctrl-X : exit

Save, load...Edit

  • Ctrl-shift-9: save structures
  • Ctrl-9: Load saved structures
  • Ctrl-S: Save solution
  • Ctrl-O: Open shared/saved solutions
  • Ctrl-H: save a picture on your desktop
  • Ctrl-shift-1/2/3: quick save 1/2/3
  • Ctrl-1/2/3: quick load 1/2/3

Mode (original interface)Edit

Menus and SelectionsEdit

  • Right-click on the segment in the original interface: open the pie menu with tools (rebuild, tweak, cut, idealize ...)
  • L: open alignment panel
  • U: open Undo menu
  • H: show menus in selection interface
  • C: cookbook in selection interface
  • V: view options in selection interface
  • B: behavior menu in selection interface
  • Ctrl-T: general options menu + release version
  • Shift-E: electron density menu
  • Shift-I: buddies
  • Shift-L: exploration map (not currently functional as of 07/16/2016)
  • A: align to the guide in selection interface
  • G: align to the guide in the original interface
  • Ctrl-A: select the entire protein in selection interface
  • Click a segment: select a segment in selection interface
  • Double-click: select a structure and the loops at each end in selection interface
  • Ctrl-click: add a segment to the selection
  • Shift-click a segment: selection of the protein from a previously clicked-on segment to the current segment in selection interface
  • Click the background: unselect all in selection interface


Move the mouse along the backbone: in the original interface, in structure mode, paint first-selected structure along the backbone

View ShortcutsEdit

  • Tab: partial score of a hovered-over segment (use arrow keys to move between segments in the original interface); template used in threading
  • Ctrl-Shift-M: revert to main style
  • General View Options:
    • Shift-C: toggle "Show clashes"
    • Shift-V: toggle "Show voids"
    • Shift-B: toggle "Show bonds (sheet)"
    • Shift-H: toggle "Show bonds (helix)"
    • Shift-R: toggle "Use relative score coloring"
    • Shift-S: toggle "Show guide"
    • Shift-F: toggle "Color relative to guide"
    • Shift-G: toggle "Hide GUI"
    • Ctrl-M: toggle "Color mutable segments"
    • Ctrl-W: toggle "Show bondable atoms"
    • Ctrl-shift-E: toggle "Show ligand constraints"
    • Shift-E : toggle "Show constraints"
    • Ctrl-D: toggle "X-ray tunnel for ligand"
    • Ctrl-I: toggle "Show isosurface"
  • Color Options:
    • Ctrl-Shift-H: enter hydrophobic view
    • Ctrl-Shift-S: enter score view
    • Ctrl-shift-U: previous color option
    • Ctrl-shift-I: next color option
  • View Protein Options:
    • Ctrl-shift-O: previous backbone view option
    • Ctrl-shift-P: next backbone view option
    • Ctrl-shift-S: tube
  • Combined Color / Protein Options:
    • Ctrl-shift-X: enzdes / cartoon thin
    • Ctrl-shift-D: CPK / line 
    • Ctrl-shift-F: CPK / line+polarH
    • Ctrl-shift-G: CPK / polarH
    • Ctrl-shift-L: score/hydro / trace line
    • Ctrl-shift-M: score/hydro / cartoon
    • Ctrl-shift-C: CPK / stick
    • Ctrl-shift-B: CPK / stick+H
    • Ctrl-shift-V: CPK / stick+polarH
  • View Sidechains Options:
    • Shift-D: select "Don't Show (Fast)"
    • Shift-T: select "Show Stubs"
    • Shift-A: select "Show All (Slow)"

Visibility ShortcutsEdit

Visibility shortcuts control how much of the protein is visible in the far and near distance. They also affect the display of the electron density cloud, if the cloud is visible.

The "focus on segment" shortcut is especially useful in electron density puzzles. It restricts the density display to the same plane as the selected segment.

The distance shortcuts, in Windows, involve holding some combination of shift, ctrl, and alt, clicking with the left mouse button and dragging the pointer upward or downward.

The shortcuts in this section work the same way in the original and the selection interfaces.

The shortcuts are:

  • Ctrl-shift-click+drag: far distance cutoff. Holding ctrl+shift and dragging the pointer downward causes the more distant parts of the protein to quickly fade and disappear. Dragging the pointer upward brings the distant parts of the protein into view.
  • Alt-shift-click+drag: distance fog or haze. Holding alt+shift and dragging the pointer downward reduces the visibility of the more distant parts of the protein. Dragging the pointer upward makes the more distant parts more visible again.
  • Ctrl-alt-click+drag: near visibility cutoff. Holding ctrl+alt and dragging the pointer upward causes the nearer parts of the protein to quickly fade and disappear. Dragging the pointer downward brings the nearer parts of the protein into view. Note that the direction of dragging is different than in the far visibility shortcuts.
  • Shift-Q: focus on segment. Hovering over a segment and hitting shift-q moves the segment to the center of the window. If an electron density cloud is visible, only the density in the same plane as the selected segment is displayed.
  • Q: recenter protein. The q shortcut resets all the visibility options to maximum visibility and focuses the display on the center of the protein. This may drastically change the display. For example, the visible portion of the electron density cloud may be moved out of view.

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