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Using the Mouse
The following functions are associated with the two-button mouse.

keyboard left buttona right buttona

- selection, X/Y rotate X/Y translate
Shift range selection, Z rotate scaling
Control multiple selection, global X/Y rotateb global X/Y translate
Control + Shift global Z rotateb scaling
Alt group picking ...
Alt ("View" mode) group selection c ...
Alt ("Build" mode) bond rotate bond stretching
Control ("Build" mode) fragment X/Y rotate fragment X/Y translate
Control + Shift ("Build" mode) fragment Z rotate scalingb

Double click
left button
Mouse Wheel

- Zooming, scroll up/down
-   "Build" Mode substitution, insertion ...
-   "Bonding" mode select atom d ...

a) Left and right buttons together with no modifier keys are used for defining a section box.
b) In this context, 'Global' means all visible molecules.
c) With both left and right mouse buttons selected a selection box for multiple object selection is available.
d) Select atom as opposed to selecting an open valence.

Mouse/keyboard operations may be broadly separated into two categories: selection (picking) and manipulation (translation/rotation).

Selection
The left button is used for picking of objects on screen and/or of menu items. Left and right buttons together are used to define a selection box for copying/cutting to the clipboard, as well as for model and color control for designated parts of a molecule. Together with the Shift key, the left button allows for picking over a range. Together with the Ctrl (Control) key, the left button allows for multiple picking. Both range and multiple picking applies not only to text items in lists, but to atoms and bonds in molecules as well. Together with the Alt key, the left button allows for selection of an entire group (detached molecular fragment).

Manipulation
The left button is used for rotation and the right button is used for translation and scaling of objects on screen. With no modifier keys, the left mouse button gives rise to rotation about the X and Y (screen) axes; the right mouse button gives rise to translation in the X and Y (screen) directions. Together with the Shift key, the left mouse button gives rise to rotation about the Z direction and the right mouse button gives rise to scaling.

The Ctrl key in conjunction with the left or right mouse buttons and (optionally) the Shift key, signifies a change in focus away from the default for the purpose of rotations and translations. Outside of "build mode", the default is focus on a single molecule (the "selected" molecule). Use of the Ctrl key changes focus to the entire set of molecules on screen, meaning that rotations and translations are carried out globally. In "build mode", the default is focus on the full set of fragments which make up the molecule being constructed, and rotations and translations refer to this set of fragments as a whole. Use of the Ctrl key changes focus to a single fragment (the "selected" fragment), and rotations and translations now refer only to this fragment.

Use of the Alt key in addition to the left mouse button allows for rotation about a "selected" bond and, in addition to the right mouse button, for stretching of the "selected" bond.