/usr/share/doc/garlic-doc/commands/col.html

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<title>
COL, color
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<h1 align=center>

COL, color

</h1>

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<font color=#880000>
<b>
NAME
<br>
</b>
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COL, color - change the color of selected atoms and their corresponding bonds.
<br><br>


<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
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COL color_scheme_name
<br>
COL left_1 middle_1 right_1 ... ... ... left_N, middle_N, right_N
<br><br>


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DESCRIPTION
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</b>
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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. From version 1.5, default color scheme is COLD.
<br><br>


<font color=#880000>
<b>
color USAGE
<br>
</b>
</font>


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:
<br><br>

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:
<br><br>

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

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


<font color=#880000>
<b>
Planes, spheres and cylinders
<br>
</b>
</font>


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.
<br><br>


<font color=#880000>
<b>
USING PREDEFINED color SCHEMES
<br>
</b>
</font>


Twenty predefined color schemes are available:
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

SCHEME NAME

</td>

<td align="left">

DESCRIPTION

</td>

<tr>

<td align="left">

RED

</td>

<td align="left">

Red color scheme; distant atoms are dark

</td>

<tr>

<td align="left">

GREEN

</td>

<td align="left">

Green, distant atoms are dark

</td>

<tr>

<td align="left">

BLUE

</td>

<td align="left">

BLUE (deep sea), distant atoms are dark

</td>

<tr>

<td align="left">

YELLOW

</td>

<td align="left">

Yellow, distant atoms are dark

</td>

<tr>

<td align="left">

CYAN

</td>

<td align="left">

Cyan (cloudless sky), distant atoms are dark

</td>

<tr>

<td align="left">

MAGENTA

</td>

<td align="left">

Magenta, distant atoms are dark

</td>

<tr>

<td align="left">

WHITE

</td>

<td align="left">

Shades of gray, distant atoms almost black

</td>

<tr>

<td align="left">

YELLOW-GREEN

</td>

<td align="left">

Somewhere between yellow and green,
<br>
distant atoms dark

</td>

<tr>

<td align="left">

CYAN-GREEN

</td>

<td align="left">

Somewhere between green and blue-green,
<br>
distant atoms dark

</td>

<tr>

<td align="left">

CYAN-BLUE

</td>

<td align="left">

Somewhere between blue and blue-green,
<br>
distant atoms dark

</td>

<tr>

<td align="left">

MAGENTA-BLUE

</td>

<td align="left">

Somewhere between blue and magenta,
<br>
distant atoms are dark

</td>

<tr>

<td align="left">

MAGENTA-RED

</td>

<td align="left">

Somewhere between red and magenta,
<br>
distant atoms are dark

</td>

<tr>

<td align="left">

ORANGE

</td>

<td align="left">

Orange, distant atoms are dark

</td>

<tr>

<td align="left">

HOT

</td>

<td align="left">

The nearest atoms are yellow, atoms in the middle are orange
<br>
and distant atoms are dark red

</td>

<tr>

<td align="left">

COLD

</td>

<td align="left">

Default color scheme: the nearest atoms are cyan, atoms in
<br>
the middle are cyan-blue and distant atoms are dark blue

</td>

<tr>

<td align="left">

MODEL

</td>

<td align="left">

Use different colors for different NMR models

</td>

<tr>

<td align="left">

MONOCHROME

</td>

<td align="left">

Edge black, central region white,

distance independent

</td>

<tr>

<td align="left">

CPK

</td>

<td align="left">

Modified Corey-Pauling-Kultun color scheme,
<br>
distant atoms are dark

</td>

<tr>

<td align="left">
size
</td>

<td align="left">
Residues are colored according to the side chain size.
</td>

<tr>

<td align="left">

ZEbrA

</td>

<td align="left">

Residues with even serial number are red, odd residues
<br>
cyan-blue, distant atoms are dark

</td>

<tr>

<td align="left">
WEIGHTED
</td>

<td align="left">
Residues are colored according to the absolute value
<br>
of weighted hydrophobicity. For more details, read
<br>
the source file color_weighted.c !
</td>

<tr>

<td align="left">
CHAIN
</td>

<td align="left">
Use color to distinguish chains;
<br>
distant atoms are should be dark
</td>

<tr>

<td align="left">
HYPHOB
</td>

<td align="left">
Assign color according to hydrophobicity;
<br>
distant atoms are dark
</td>

</table>


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


<img src="colors.png">


<br><br>


<font color=#880000>
<b>
DETAILED color SPECIFICATION
<br>
</b>
</font>


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:
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

col yellow orange red red DarkRed black

</td>

<td align="left">

Define two color surfaces
<br>
with six colors.

</td>

<tr>

<td align="left">

col rgb:ffff/ffff/4444 rgb:ffff/dddd/0000 DarkRed

</td>

<td align="left">

One color surface,
<br>
three colors.

</td>

<tr>

<td align="left">

col old old old black black black

</td>

<td align="left">

Leave the front colors unchanged,
<br>
set all back colors to black.

</td>

</table>

<br>


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.
<br><br>


<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>


FADING may be used to change the position of outer color surfaces and to
switch color fading on and off.
<br><br>


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garlic-doc 1.6-1 / usr / share / doc / garlic-doc / commands / col.html
