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<head>
<title>
FAD, FADING
</title>
</head>
<h1 align=center>
FAD, FADING
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
FAD, FADING - change the color dependence on a distance from the observer.
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
FAD keyword
<br>
FAD FRONT shift
<br>
FAD BACK shift
<br>
FADING keyword
<br>
FADING FRONT shift
<br>
FADING BACK shift
<br><br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
Change the way color depends on distance. Distance is measured from the
atom to the observer. This command comes in three versions:
<br><br>
(1) FADING FRONT shift ----> move the front color surface;
<br>
(2) FADING BACK shift ----> move the back color surface;
<br>
(3) FADING keyword ----> switch fading off or change the type of the surfaces.
<br><br>
<font color=#880000>
<b>
FADING FRONT shift
<br>
</b>
</font>
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.
<br><br>
<font color=#880000>
<b>
FADING BACK shift
<br>
</b>
</font>
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.
<br><br>
<font color=#880000>
<b>
FADING keyword
<br>
</b>
</font>
Some keywords may be used to change the type of color surfaces and to switch
color fading off. Here is the list of keywords:
<br><br>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
SHORT FORM
</td>
<td align="left">
LONG FORM
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
OFF
</td>
<td align="left">
OFF
</td>
<td align="left">
Switch fading off:
<br>
colors should become distance independent
<br>
</td>
<tr>
<td align="left">
PLA
</td>
<td align="left">
PLANE
</td>
<td align="left">
Use planes as color surfaces
</td>
<tr>
<td align="left">
SPH
</td>
<td align="left">
SPHERE
</td>
<td align="left">
Use spheres as color surfaces
</td>
<tr>
<td align="left">
CYL
</td>
<td align="left">
CYLINDER
</td>
<td align="left">
Use cylinders as color surfaces
</td>
<tr>
<td align="left">
HALF-SPH
</td>
<td align="left">
HALF-SPHERE
</td>
<td align="left">
Use spheres as color surfaces, but apply
<br>
only to the front half of the structure.
</td>
<tr>
<td align="left">
HALF-CYL
</td>
<td align="left">
HALF-CYLINDER
</td>
<td align="left">
Use cylinders as color surfaces, but apply
<br>
only to the front half of the structure.
</td>
</table>
<br>
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 user's standpoint).
<br><br>
<font color=#880000>
<b>
EXAMPLES
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
COMMAND
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
fading off
</td>
<td align="left">
Switch color fading off
</td>
<tr>
<td align="left">
fading front 4.5
</td>
<td align="left">
Move the front color surface 4.5 angstroms
<br>
away from the observer
</td>
<tr>
<td align="left">
fading back -2.8
</td>
<td align="left">
Move the back color surface 2.8 angstroms
<br>
closer to the observer
</td>
<tr>
<td align="left">
fading half-sph
</td>
<td align="left">
Change fading to semi-spherical
</td>
</table>
<br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
color defines the color for selected atoms.
<br><br>
<hr size="3">
</html>
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