Garlic Configuration File - Version 1.5


garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page contains the sample configuration file for garlic. When started, garlic will try to find the configuration file called .garlicrc (or garlicrc, in one case!) in up to seven directories, in the following order:

(1) in the current working directory (file .garlicrc);
(2) in user's home directory ($HOME/.garlicrc);
(3) in garlic subdirectory of user's home directory ($HOME/garlic/.garlicrc);
(4) in /usr/share/garlic directory; recommended as the system-wide configuration directory;
(5) in /etc directory (Debian GNU/Linux style, /etc/garlicrc, without dot!);
(6) in /usr/local/lib/garlic directory (file /usr/local/lib/garlic/.garlicrc);
(7) in /usr/lib/garlic directory (file /usr/lib/garlic/.garlicrc).

The recommended pathnames:

/usr/share/garlic/.garlicrc (system-wide configuration file),
$HOME/.garlicrc (private configuration file).

Many users can't use the commands create and replace, because they don't have the file residues.pdb, or they can't customize the program because they don't know where to find the configuration file (.garlicrc).
Read this text , please, for more details!
There is a chance that files .garlicrc and residues.pdb are already installed on your system. Use the command locate to check this:
man locate (to learn something about the command locate);
locate .garlicrc
locate residues.pdb

If all attempts fail, the hard-coded defaults will be used. The configuration file .garlicrc should be included in the original garlic package. Most parameters are explained below (read the comments). Anyway, if you have some questions, send an e-mail to me:
# Personal initialization file for garlic, free molecular viewer and editor.
# Version 1.5.
# Last modification: January 12, 2006.

# Geometry of the main window. Use the keyword default, or specify the
# geometry string (for example 780x560+10+10).

main window geometry: default

# Margins; used only if geometry string is not given. Geometry string may be
# given through command line arguments.

main window left margin: 50 pixels
main window right margin: 50 pixels
main window top margin: 50 pixels
main window bottom margin: 70 pixels

# Main font:

main font: 10x20

# Main window cursor. If you don't like default cursor, replace it; read
# the file /usr/include/X11/cursorfont.h ; remove the XC_ prefix to obtain
# the cursor name.

main window cursor: default

# A small coordinate system may be displayed in the top left corner (yes/no):

show coordinate system: yes

# Control window (top right corner) may be visible or hidden (yes/no):

show control window: yes

# Sequence neighborhood of the residue under the pointer may be hidden,
# visible and short or visible and verbose (no/yes/verbose):

show sequence neighborhood: verbose

# Stereo flag (yes/no):

display stereo image: no

# Parameters for stereo image:

stereo internal margin (screen units): 10 pixels
stereo angle: 5.0 degrees

# Light source theta and phi angle (theta is defined with respect to z axis,
# phi with respect to x axis:

light source theta angle: 150 degrees
light source phi angle:   225 degrees

# Default slab mode (possible modes are off, planar, sphere, half-sphere,
# cylinder and half-cylinder):

default slab mode: planar

# Default color fading mode (off, planar, sphere, half-sphere, cylinder and
# half-cylinder): 

default color fading mode: planar

# Default drawing style for atoms (0, 1, 2, 3, 4, 5, 6 or 7):

default atom drawing style: 2

# Default drawing style for bonds (0, 1, 2, 3, 4 or 5):

default bond drawing style: 3

# Default drawing style for backbone:

default backbone drawing style: 5

# Window colors:

main window background color: black
main window foreground color: white
text background color: black
text foreground color: white

# The number of color fading surfaces:

number of color fading surfaces: 3

# Default colors for atoms and bonds. For each fading surface, three colors
# should be specified. The surface index is a small integer following the
# word color. The largest surface index is equal to:
# (number of color fading surfaces) - 1,
# which is in this case 2. Color may be changed at runtime, of course.
# This choice of colors is equivalent to the color scheme COLD.

left   color 0: RGB:DDDD/FFFF/FFFF
middle color 0: RGB:0000/FFFF/FFFF
right  color 0: RGB:0000/8888/FFFF

left   color 1: RGB:0000/8888/FFFF
middle color 1: RGB:0000/0000/FFFF
right  color 1: RGB:0000/0000/8888

left   color 2: RGB:0000/0000/8888
middle color 2: RGB:0000/0000/4444
right  color 2: RGB:0000/0000/2222

# Default color schemes for molecular surfaces. Choose from this list:
# red, green, blue, cyan, magenta, yellow, white, orange,
# cyan-blue, cyan-green, yellow-green, magenta-blue, magenta-red,
# orange-yellow, orange-red. Do not use the following color schemes:
# hot, cold, monochrome, cpk, zebra, chain, hyphob and model.

surface outer color scheme: magenta
surface inner color scheme: blue

# Rotation steps. Normal steps is used if numeric key is pressed without
# any modifier. Large step is selected by holding [shift] while pressing
# the key, and very large step is selected by using both [alt] and [shift].
# Small step is selected by holding [control] while pressing the key, and
# very small step by using both [alt] and [control].

rotations steps: 0.2 1.0 5.0 30.0 90.0

# Five translation steps (very small, small, normal, large and very large).
# Use angstrom units.

translation steps: 0.2 1.0 5.0 25.0 100.0

# Five slab steps (very small, small, normal, large and very large).
# Use angstrom units.

slab steps: 0.2 1.0 5.0 20.0 80.0

# Five fading steps (very small, small, normal, large and very large).
# Use angstrom units.

fading steps: 0.2 1.0 5.0 20.0 80.0

# Window size limits: used only if screen width and/or height are larger
# than values specified here. By default, screen width and height are used.

maximal main window width: 3000 pixels
maximal main window height: 2500 pixels

# The nearest line (bond) thickness; used only if drawing bonds as lines
# and line thickness is used for perspective.

the nearest line thickness: 5 pixels

# Screen dimensions and position of garlic user in real world. Use realistic
# values. Do not change units (mm). Strange values may cause image distortions.

screen width in real world: 270 millimeters
screen height in real world: 195 millimeters
distance between user and screen in real world: 500 millimeters

# Scaling information: used to scale user and screen down to atomic scale.
# Only screen width is required, in angstrom units.

screen width in atomic world: 1.0 angstroms

# User z coordinate in atomic coordinate system. It must be negative
# and absolute value should be quite large. The x axis points to the right,
# y axis downward and z axis in direction opposite to observers direction.

user position in atomic coordinate system: -150.0 angstroms

# Maximal bond length is used to check which atoms and bonds are invisible.
# It is assumed that there are no atoms with radius larger than this length.

maximal bond length: 2.3 angstroms

# Crude limits for bond lengths. No distinction between N-CA and C-N is made.
# Use angstrom units. Be tolerant, there are many bad structures around.
# Generic bond length is used for atomic pairs which are not recognized.

approximate C-C bond length: from 1.3 to 1.8 angstroms
approximate C-N bond length: from 1.0 to 1.7 angstroms
approximate C-O bond length: from 1.0 to 1.7 angstroms
approximate C-S bond length: from 1.4 to 2.1 angstroms
approximate C-H bond length: from 0.8 to 1.2 angstroms
approximate N-O bond length: from 1.2 to 1.7 angstroms
approximate N-H bond length: from 0.9 to 1.3 angstroms
approximate O-H bond length: from 0.7 to 1.3 angstroms
approximate S-H bond length: from 0.9 to 1.6 angstroms
approximate O-P bond length: from 1.2 to 1.8 angstroms
approximate S-S bond length: from 1.8 to 2.3 angstroms
generic bond length:         from 0.8 to 2.0 angstroms
hydrogen bond length:        from 2.0 to 5.0 angstroms

# Hydrogen bond C-O...N angle range (obsolete since version 1.3!):

hydrogen bond C-O...N angle: from 125 to 180 degrees

# The upper limit for CA-CA distance for neighbouring residues. Used to
# draw backbone, connection neighbouring CA atoms.

maximal CA-CA distance: 4.1 angstroms

# Atomic radii, used for spacefill style. 70% of van der Waals radius may be
# a good choice.

hydrogen radius:   0.70 angstroms
carbon radius:     1.20 angstroms
nitrogen radius:   1.05 angstroms
oxygen radius:     1.00 angstroms
sulfur radius:     1.25 angstroms
phosphorus radius: 1.25 angstroms
generic radius:    1.40 angstroms

# Covalent atomic radii, used for covalent style.

hydrogen covalent radius:   0.30 angstroms
carbon covalent radius:     0.77 angstroms
nitrogen covalent radius:   0.70 angstroms
oxygen covalent radius:     0.66 angstroms
sulfur covalent radius:     1.04 angstroms
phosphorus covalent radius: 1.10 angstroms
generic covalent radius:    1.20 angstroms

# Small atomic radii. 70% of covalent radius may be a good choice.

hydrogen small radius:   0.21 angstroms
carbon small radius:     0.54 angstroms
nitrogen small radius:   0.49 angstroms
oxygen small radius:     0.46 angstroms
sulfur small radius:     0.73 angstroms
phosphorus small radius: 0.77 angstroms
generic small radius:    0.84 angstroms

# Van der Waals radii.

hydrogen van der Waals radius:   1.00 angstroms
carbon van der Waals radius:     1.70 angstroms
nitrogen van der Waals radius:   1.50 angstroms
oxygen van der Waals radius:     1.40 angstroms
sulfur van der Waals radius:     1.80 angstroms
phosphorus van der Waals radius: 1.80 angstroms
generic van der Waals radius:    2.00 angstroms

# Default ball radius (used to draw atoms as balls of equal size):

default ball radius: 0.40 angstroms

# Default bond probe radius, used to draw nice bonds with curved surfaces:

default bond probe radius: 0.80 angstroms

# Default stick radius, used to draw bonds as sticks:

default stick radius: 0.15 angstroms

# For a given atom, the chemical bonds are identified by inspecting
# distances to the neighboring atoms. The array with atomic data should
# be scanned in forward and backward direction (with respect to the given atom)
# to find which atoms are bound to the given atom. The following parameters
# define how many neighboring atoms should be checked in each direction.

number of bond candidates: 50 before and 50 after the given atom

# Blur rectangle width and height (default values). Bluring is used to reduce
# the contrast. The color of the pixel in the center of the rectangle is
# calculated by averaging the colors of all pixels in the rectangle. Both
# values should be positive integers.

blur rectangle width:  3
blur rectangle height: 3