The Display menu

In this menu display settings/styles can be changed.

In general, display styles are applied to the currently selected set of atoms and bonds.

By default, all atoms and bonds in a molecule are selected.

You may select individual atoms/bonds by using the selection cursor or by using script commands.

Atom Style

Quick Draw

Renders atoms as filled circles.

Shaded

Renders atoms as shaded spheres.

Wire Frame

Renders atoms as circle outlines.

Invisible

Atoms are not drawn, but are assumed to have the same radius that they would occupy. So bonds are drawn to the outer circumference of where the atom would be. Compare with *None*

This option can be useful when used in conjunction with atom labels to display atom type.

None

Atoms are not drawn and are assumed to have a radius of zero. Bonds are drawn to atom centers.

This option can be very useful when use in conjunction with atom labels to display atom type.

Bond Style

Quick Draw

Renders bonds as filled rectangles.

Shaded

Renders bonds as shaded cylinders.

Wire Frame

Renders bonds as lines.

Boxes

Renders bonds as rectangle outlines. (deprecated)

None

Bonds are not drawn.

Atom Labels

None

No atom labels is shown.

Atomic Symbols

Atoms are labeled with their atomic symbol.

Atom Types

Atoms are labeled with their atom type. (What is the difference between Atom Type and Atom Symbol?)

Atom Numbers

Atoms are labeled with index numbers.

Atom Coloring

Atom Type

Atoms are colored based upon their type. Default colors are generally CPK colors

Atomic Charge

Atoms are colored based upon atomic charge. (Need more explanation here!)

Wireframe Rotation

This option may be checked if performance is unacceptable when manipulating large molecules. When this option is checked, wireframe rendering is used for displayed atoms and bonds during rotations, translations, and zoom operations. The molecule is rendered according to the current settings when the mouse is released.

Perspective Depth

This option controls rendering with perspective depth. When this option is unchecked molecules are rendered as an orthogonal flat projection onto the screen. When this option is checked, sizes and distances are adjusted for a camara perspective.

For a good example of this take a look at some of the crystal structures, such as samples/CdSe_nanocrystal.xyz or samples/HfO2_on_Si_relax.in

Alternatively, you can turn on the bounding box to see the effect of this setting (see below).

Axes

Displays cartesian axes with the origin at the center of the bounding box defined by the extreme coordinates of the molecule.

Note that the positive Y axis is at the top, unlike RasMol.

Bounding Box

Displays the bounding box, defined by the extreme coordinates of the centers of the atoms in each of the three dimensions.

Hydrogens

Turns on/off the display of hydrogen atoms.

Vectors

Controls the display of vibrational vectors as dipole moments.

Measurements

Controls the display of distance, angle, and dihedral torsion measurements.