COL, COLOR

NAME
COL, COLOR - change the color of selected atoms and their corresponding bonds.

SYNOPSIS
COL color_scheme_name
COL left_1 middle_1 right_1 ... ... ... left_N, middle_N, right_N

DESCRIPTION
Change the color used to draw selected atoms and their corresponding bonds. Half of each bond belongs to one atom, while half of the same bond belongs to another atom. The easy way to specify color is to use the predefined color scheme. The powerfull (but more complicated) way to specify color is to issue detailed color specification.

COLOR USAGE
In garlic, colors are used to create 3D illusions. In most color schemes, the atoms close to the observer have bright colors, while distant atoms have dark colors. Atoms and bonds look like three-dimensional objects because one side is brighter than the other. Here are some technical details about color usage:

At least one and at most eight surfaces are assigned to each structure. These surfaces are equidistant planes, spheres or cylinders. The surface which is nearest to the observer is called "front surface", while the most distant surface is called "back surface". To each surface, three colors are assigned: left, middle and right color. In most color schemes, left color is bright and right color is dark. Atoms may be divided in three groups:

(1) Atoms which are in front of the front surface;
(2) Atoms which are behind the back surface;
(3) All other atoms, positioned in the sandwich between two surfaces.

All atoms which are in front of the front surface are drawn using the same set of three colors which assigned to front surface. Atoms behind the back surface are colored using three colors assigned to back surface. Colors for atoms laying between two surfaces are prepared by linear interpolation of colors assigned to these two surfaces. This is what I call color fading (this term was not the best choice I could make, sorry).

In a special case, when only one surface is used, color does not depend on distance.

Almost all predefined color schemes typically define two surfaces, i.e. a total of six colors. There are some exceptions: color schemes HOT and COLD use three surfaces, while MONOCHROME uses only one.

Planes, spheres and cylinders
For most proteins and other molecules, planar fading is the best choice. In this case, a set of planes, perpendicular to z axis is used. Concentric spheres may be used when working with large globular proteins, while cylinders may be used for beta-barrel proteins, like porins. The axis of concentric cylinders is parallel to y.

USING PREDEFINED COLOR SCHEMES
Twenty predefined color schemes are available:

SCHEME NAME DESCRIPTION
RED Red color scheme; distant atoms are dark
GREEN Green, distant atoms are dark
BLUE BLUE (deep sea), distant atoms are dark
YELLOW Yellow, distant atoms are dark
CYAN Cyan (cloudless sky), distant atoms are dark
MAGENTA Magenta, distant atoms are dark
WHITE Shades of gray, distant atoms almost black
YELLOW-GREEN Somewhere between yellow and green,
distant atoms dark
CYAN-GREEN Somewhere between green and blue-green,
distant atoms dark
CYAN-BLUE Somewhere between blue and blue-green,
distant atoms dark
MAGENTA-BLUE Somewhere between blue and magenta,
distant atoms are dark
MAGENTA-RED Somewhere between red and magenta,
distant atoms are dark
ORANGE Orange, distant atoms are dark
HOT The nearest atoms are yellow, atoms in the middle are orange
and distant atoms are dark red
COLD The nearest atoms are cyan, atoms in the middle are cyan-blue
and distant atoms are dark blue
MODEL Use different colors for different NMR models
MONOCHROME Edge black, central region white, distance independent
CPK Modified Corey-Pauling-Kultun color scheme,
distant atoms are dark
ZEBRA Residues with even serial number are red, odd residues
cyan-blue, distant atoms are dark
CHAIN Use color to distinguish chains;
distant atoms are should be dark
HYPHOB Assign color according to hydrophobicity;
distant atoms are dark

Do not abbreviate the color scheme name! Case is not important. Some selected schemes are shown below.



DETAILED COLOR SPECIFICATION
Most users should be satisfied with predefined color schemes. Anyway, it is fairly easy to use colors which are not available through predefined schemes. To define N color planes (up to eight), you have to define 3 * N colors. The keyword OLD may be used to leave the previous value unchanged. Here are some examples:

col yellow orange red red DarkRed black Define two color surfaces
with six colors.
col rgb:ffff/ffff/4444 rgb:ffff/dddd/0000 DarkRed One color surface,
three colors.
col old old old black black black Leave the front colors unchanged,
set all back colors to black.

Be careful with the keyword OLD - it may be used only if the currently used color scheme has at least as many colors as a new one.

RELATED COMMANDS
FADING may be used to change the position of outer color surfaces and to switch color fading on and off.