Chapter 5
Molecular Drawing Methods
5.1
Molecular Drawing Methods
JMV allows you to view the molecule with different representations. To change the representa-
tion, select “Representation” from the “View” menu, and select one of the choices. The current
representations available are:
5.1.1
Lines
The default representation is ‘Lines’, which is also known as ‘wireframe’. It draws a line between
each atom and the atoms to which it is bonded. The first half of each bond is colored appropriately
for the first atom, while the color of the final half corresponds to the second atom.
5.1.2
Bonds
Nearly everything about this option is the same as lines except that instead of drawing a bond as
a line between two atoms, a cylinder is drawn instead.
5.1.3
CPK
CPK is a combination of “Bonds” and “VDW” in that it draws the atoms as spheres and also draws
the bonds connecting them. The sphere are drawn much smaller than in VDW, and the cylinders
are thinner than in Bonds. Each sphere is drawn with a radius that depends on the atom type.
5.1.4
VDW
VDW draws the atoms as spheres. Each sphere is drawn with a radius that depends on the atom
type.
5.1.5
Licorice
‘Licorice’ draws the atoms as spheres and the bonds as cylinders. The difference between this and
‘CPK’ is that the sphere radii are all the same, and are the same size as the bond.
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