B Quick Reference

The Tool Bar and Menu Bar of B.

Menu Bar

Tool Bar - Tool Bar objects are selected by left-clicking on the object.

Rotate - Once selected, rotates the molecule by holding the left mouse button down and dragging over the B screen area. Double-clicking reverts the molecule to its original orientation.
Translate - Once selected, translates the molecule by holding the left mouse button down and dragging over the B screen area. Double-clicking translates the molecule back to its original position ( usually centered ).
Zoom - Once selected, zooms the molecule in to the viewer by holding the left mouse button down and dragging the mouse to the right in the B screen area. The molecule is zoomed away from the viewer by dragging to the left. Double-clicking resets the zoom to its default value.
Selection Pointer - Once selected, left clicking on atoms results in those atoms being selected.
Selection Lasso - Left click and drag to select groups of atoms by enclosing them in a simple closed path.
Atom Label - Identify an atom by left clicking on it. The atom name is given first, followed by the atom number in parentheses, the AMBER atom type in brackets [], and the atomic charge in <>. For example, a hydrogen atom named H2 which is atom number 5 in the molecule, is AMBER atom type HO, and has charge 0.3e is displayed as H2(5)[HO]<0.3>.
Atom Labels - Labels all the atoms in the molecule using the format described above.
Build - Create new atoms and bonds clicking on this tool.
Coordinates - Once selected, left-clicking on an atom results in the x, y, and z coordinates of the atom to be displayed.
Distance - Once selected, left-clicking on two atoms results in the display of the distance between the atoms.
Angle - Display the angle between three atoms by left clicking on each ( in order ).
Torsion - Display the torsion between four atoms by left-clicking on each ( in order ).
Stop - Stops the current calculation ( not yet functional ).