FAD, FADING

NAME
FAD, FADING - change the color dependence on a distance from the observer.

SYNOPSIS
FAD keyword
FAD FRONT shift
FAD BACK shift
FADING keyword
FADING FRONT shift
FADING BACK shift

DESCRIPTION
Change the way color depends on distance. Distance is measured from the atom to the observer. This command comes in three versions:

(1) FADING FRONT shift ----> move the front color surface;
(2) FADING BACK shift ----> move the back color surface;
(3) FADING keyword ----> switch fading off or change the type of the surfaces.

FADING FRONT shift
This command moves the front fading surface. It is recommended to use this command in scripts - in interactive mode, use controls (keys F1 and F2). The shift value should be given in angstroms. Positive shift moves the front color surface away from the observer. With most color schemes, the front (closer) portion of the structure will be brighter after the positive shift. FRONT may be abbreviated to FRO.

FADING BACK shift
This command moves the back fading surface. It is recommended to use this command in scripts - in interactive mode, use controls (keys F3 and F4). The shift value should be given in angstroms. Positive shift moves the back color surface away from the observer. With most color schemes, the contrast will be reduced after the positive shift. Negative shift results in better contrast, i.e. distant atoms will become darker. BACK may be abbreviated to BAC.

FADING keyword
Some keywords may be used to change the type of color surfaces and to switch color fading off. Here is the list of keywords:

SHORT FORM	LONG FORM	DESCRIPTION
OFF	OFF	Switch fading off: colors should become distance independent
PLA	PLANE	Use planes as color surfaces
SPH	SPHERE	Use spheres as color surfaces
CYL	CYLINDER	Use cylinders as color surfaces
HALF-SPH	HALF-SPHERE	Use spheres as color surfaces, but apply only to the front half of the structure.
HALF-CYL	HALF-CYLINDER	Use cylinders as color surfaces, but apply only to the front half of the structure.

For most structures, the planar fading is the best choice. Spherical and semi-spherical fading may be useful when working with large globular proteins, while cylindrical and semi-cylindrical fading is useful when working with beta-barrel proteins (like porins). The cylinder axis is parallel to y axis (vertical from users standpoint).

EXAMPLES

COMMAND	DESCRIPTION
fading off	Switch color fading off
fading front 4.5	Move the front color surface 4.5 angstroms away from the observer
fading back -2.8	Move the back color surface 2.8 angstroms closer to the observer
fading half-sph	Change fading to semi-spherical

RELATED COMMANDS
COLOR defines the color for selected atoms.