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Coloring Molecules and Objects

 

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

There are 98 colors available in VMD, with color ids 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 indicies 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 three ranges with the color form or the text command: red->green->blue, red->white->blue, or black->white. There are no names for the specific colors.

Each color has 6 properties which consist of floating point values from 0 to 1. Some describe the color, others the transparency, and still others how the color interacts with the lights. They are:

(Note: Only the RGB value is used when rendering a molecule.)

For example, there is a Resname color category, and withing this category there are many names; one for each of the available residues names. Some of these are ALA, CYS, and PRO. Each name can be assigned a color from a list of 16 available colors called the   color map. The RGB value of each color can be modified directly in the Color form. Also, each colors has a semi-transparent version used when the transparent button is pressed in the Graphics form. To color items in a gradation manner, there are an additional 32 colors used in the color scale.

The different color categories in VMD are listed in table 6.1. The Color form is used to change the assigment of colors to the names in each of these categories. For example, to change the color used to draw Arginine residues when molecules are colored by residue, you would use the Color form, select the `Resname' category, select the `Arg' name there, and then pick the color to use for Arginine's from the list of colors next to the names.

  
Table 6.1: Color categories used in VMD .





next up previous contents index
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Andrew Dalke
Tue May 14 16:49:45 CDT 1996