B Quick Reference
The Tool Bar and Menu Bar of B.
File - The File
Menu provides the following options:
New : Erases and
deletes the current molecule.
Open : Opens a PDB
file from the local hard drive.
Save : Saves the
molecule to the local hard drive in PDB format.
Save As : Saves the
molecule to the local hard drive in PDB format. Necessary if you wish
to rename the molecule.
Print : Prints the
Triggers a dialog which allows for some user preferences to be set.
Export : Writes the
current images as a .jpeg, .gif, or .ppm file.
Exit : Exits B.
Select by : Use to mouse to select atoms, residues,
strands, or the entire molecule.
Select All : Select all the atoms in the molecule.
Invert Selection : Causes unselected atoms to be
selected and vice-versa.
Cut : Deletes current selection and places the object in
a buffer ( not yet functional ).
Copy : Copies the current selection and places the
object in a buffer ( not yet functional ).
Delete : Deletes atom or bond ( depending on which is
clicked on ).
Hide : Prevents current selection from being displayed ( not
yet functional ).
Paste : Pastes object in buffer to clicked location on
screen ( not yet functional ).
Calculate Net Mass : Returns the mass of the current
molecule in amu.
Calculate Net Charge : Returns the charge of the
molecule in e.
Calculate Energy : Performs a single-point calculation
of the gradient and energy using AMBER.
Invert Chirality : Reflects the molecule through the
z-axis, giving the stereoisomer.
Show Periodic Table :
Allows the default drawing element to be changed. Left-clicking on an
element in the periodic table results in that element being illuminated
in red. This is the new default drawing element. Now, all drawn atoms
will be of this type ( until a new default element is selected ).
Add Hydrogens : Adds hydrogens to
carbon, nitrogen, and oxygen atoms.
Add Functional Group : Attaches a
functional group to an existing molecule or places the fragment on the
Add Hydrocarbon : Attaches a
hydrocarbon to an existing molecule or places the fragment on the
Add Ring : Attaches a ring
structure to an existing molecule or places the fragment on the canvas.
Add Miscellaneous : Attaches
miscellaneous a structure to an existing molecule or places the
fragment on the canvas.
Polynucleotide - Displays a dialog
to construct a polynucleotide ( DNA or RNA ).
Polypeptide - Displays a
polypeptide dialog to construct polypeptides.
Polysaccharide - Displays a
polysaccharide dialog to construct polysaccharides.
Force Field - Select the potential energy function to
use ( force field ). Currently, only AMBER is implemented.
Minimizer - Choose either the
conjgate gradient or steepest descent technique.
Minimize - Optimize the geometry
of the molecule.
Options - Set the options for the
MD / simulated annealing run.
Start Trajectory - Start the MD /
simulated annealing run using the options above.
Render - Choose several different
Depth Cueing - Toggle depth-cueing
for the wireframe models.
Shiny - Create a "shiny"
effect on the spacefill, spheres, ball-and-stick, and polytube models.
About - Information about B.
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.
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
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
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.
Create new atoms and bonds clicking on this tool.
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.
- Display the angle between three atoms by left clicking on each ( in
Torsion - Display the torsion between four atoms
by left-clicking on each ( in order ).
Stops the current calculation ( not yet functional ).
To create a new atom:
Left-click in the B screen area. A new atom has been placed. You
may wish to have the labels turned on, so that the atom is visible. The
element is carbon, by default. The default element can be changed by
selecting a new atom from Show
To bond two atoms together: Left-click in the B screen area to place a new
atom. Continue holding the left mouse button down while dragging to the
atom to which you wish to make a bond.
To move an atom: Hold
the middle-mouse button down and drag to the desired location.
To change the bond order: To change between single, double, and triple bonds,
right-click on the bond, and the bond order will cycle between single,
double, and triple bonds.
To change the atom type: To change the atom type, select a
new atom from Show Periodic Table,
and left-click on the atom to be replaced.