Chem3D Users Manual - CambridgeSoft

Administrator
Surface Type
Solid
Description
The surface is
displayed as an opaque
form. Solid is a good
choice when you are
interested in the details
of the surface itself,
and not particularly
interested in the
underlying atoms and
bonds.
Surface Type
Translucent
Description
The surface is
displayed in solid
form, but is partially
transparent so you can
also see the atoms and
bonds within it.
Translucent is a good
compromise between
surface display styles.
Setting Molecular Surface Isovalues
Wire Mesh
Dots
The surface is
displayed as a
connected net of lines.
Wire Mesh is a good
choice when you want
to focus on surface
features, but still have
some idea of the atoms
and bonds in the
structure.
The surface is
displayed as a series of
unconnected dots.
Dots are a good choice
if you are primarily
interested in the
underlying structure
and just want to get an
idea of the surface
shape.
Isovalues are, by definition, constant values used to
generate a surface. For each surface property, values
can be calculated throughout space. For example,
the electrostatic potential is very high near each
atom of a molecule, and vanishingly small far away
from it. Chem3D generates a surface by connecting
all the points in space that have the same value, the
isovalue. Weather maps are a common example of
the same procedure in two dimensions, connecting
locations of equal temperature (isotherms) or equal
pressure (isobars).
To set the isovalue:
1. From the Surfaces menu, choose Isocontour.
NOTE: The exact name of this command reflects the
type of isovalue in each window. For example, for Total
Charge Density Surfaces, it is “Isocharge”.
The Isocontour slider appears.
2. Adjust the slider to the new isovalue.
The new isovalue is the middle value listed at
the bottom of the Isocontour tool.
66 •Displaying Models CambridgeSoft
Molecular Surface Displays