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VMD maintains a database of the colors used for the molecules and
other graphical objects which are visible in the display window. It
keeps track of
- color name definitions - RGB, alpha value, etc.
- mappings from a color category to color name - so residue name
MET is colored yellow
- the current color scale - red to white to blue, and several related parameters
There are 98 colors available in VMD, with color ids ranging from 0 to
97. Of these, 34 are named. The first 17 (with values 0 to 16) are,
in order: blue, red, gray, orange, yellow, tan, silver, green, white,
pink, cyan, purple, lime, mauve, ochre, iceblue, and black. The next
17 (with color indices from 17 to 33) are translucent (partially
transparent) versions of the same terms. The names for these are the
same as the solid color, prefixed with the word ``trans_''. For
example, the translucent version of ``yellow'' is ``trans_yellow''.
The next group of 32 colors (from 34 to 65) are solid colors used in
the color map, followed by the 32 colors (65 to 97) which make up the
translucent forms of the solid colors. These can be set to one of
several ranges with the Color form or the color text command:
red 
green blue,
red white blue, or black white,
etc. There are no names for the specific colors. The color map will
be discussed in more detail in a section to follow.
Each color has six properties which consist of floating point values.
Some describe the color, others the transparency, and still others how
the color interacts with the surrounding light. For the most part, you
will not need to alter the values given to these parameters by
default. Alterations will usually only arise when you want to tweak
values to output rendering files used by VRML and POV readers.
Another application of changing the default color settings might be
defining your own color palette or making black-and-white pictures.
The six options are:
- RGB: a triplet of numbers (0.0 to 1.0) describing the color
(red, green, blue);
0 indicates none of that color (also see Diffuse).
- Alpha: a number (0.0 to 1.0) describing the transparency;
1 is solid, 0 is transparent. By default, transparent objects
are drawn with alpha set to .3
- Ambient: a triplet of numbers (0.0 to 1.0) describing RGB values
for the ambient light for the given color. Noticeable in
absence of diffuse light. Ambient light
provides a uniform illumination of objects with a
background lighting of the specified color. This means
that if you have ambient for the color named 'cyan' set to 1 0
0, the object colored in 'cyan' will appear red in the
absence of any light sources and will have a red component
in the 'shaded' areas in the presence of light sources.
Default is (0.0, 0.0, 0.0).
- Diffuse: same as RGB; This property determines the color of the
object. Diffuse reflections are independent of the viewing
direction, but depend on the direction of the light source
with respect to the surface of the displayed object.
- Specular: a triplet of numbers (0.0 to 1.0) describing the color of
specular reflections. Produces highlights, the higher the
value, the smaller and the brighter the highlight.
Default is (1.0, 1.0, 1.0). You can reduce
the reflectivity of the surface by reducing all three
values (say, to 0.5 0.5 0.5). This would give white light
reflections with less intensity. However, you can use any
settings to produce effect of a colored reflection.
- Shininess: a number (1 to 100) describing how large is the angle of
the specular reflections. The smaller the number the
wider the angle and the more shiny objects appear.
Default is 40.
For details regarding these material properties, consult an elementary
graphics book such as Foley & Van Dam (Computer Graphics).
Next: 6.1 Color categories
Up: No Title
Previous: 5.16 Off
Sergei Izrailev
Fri Jul 25 17:07:27 CDT 1997