VMD maintains a database of the colors used for the molecules and the other graphical objects in the display window. The database consists of several color categories; each color category contains a list of names, and each name is assigned a color. The assignment of colors to names can be changed with this form. There are 16 colors, as well as black (the VMD color map), and this form can also be used to modify the definitions of these 17 colors. For more about colors, see the chapter on Coloring.
To see the names associated with a color category, click on the category in the Category browser located on the left side of the form. Click on the name to see the color to which it is mapped. To change the mapping, click on a new color in the browser to the right of the Category browser. For instance, to change the background to white, pick `Display' in the left browser and `Background' in the center one. The right browser will indicate the current color (which is initially black for the background). Scroll through the right browser and select white to change the background.
Sometimes you may want to change the RGB value of a color in the color map, instead of changing which color is assigned to a particular name. For example, you may need to make a black and white picture and need to emphasize the contrast between a red oxygen and a yellow sulphur. This is done with the Edit Colors part of the form. First, choose the color you want changed in the browser. Then move the red, green, and blue sliders until you get the desired color. There are a few additional buttons to help you do this. The white button makes the color white (red = blue = green = 1.0) and the black color makes it black (red = blue = green = 0.0). The default button restores the color to its original RGB values. The tie button is used to make grey colors; when the button is depressed, as you move one slider the rest will follow. Press the tie button again to untie the sliders.
For example, suppose, we don't really like the appearance of the green color and we want to make it darker. To see what is happening we'll change the color of the background, so choose Display in the category field of the upper part of the Color form, then choose Background, and, finally, choose green. The background should become green. The (default) RGB values are 0.20, 0.70, 0.20. To make the color darker, let's bring the RGB values down by moving the red, green and blue sliders to the left. You can see the color changing as you move the sliders, so this way you can easily pick the color you prefer to be named 'green'. The definition can be immediately brought back to the default values by pressing the 'Default' button on the form.
Several of the coloring methods in the graphics form are used to color a range of values, as compared to a list of names. The actual coloring is determined by the color scale.
There is only one color scale available at any one time (out of the ten possible) and it is changed with the Color Scale Method chooser. Changing the values of Minimum and Midpoint change some of the proportionality values used in making the scale.
The colors used by the color scale are not the colors in the color map, so the Edit Colors part of the form will not affect the color scale colors.
