Garlic Configuration File


garlic, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software, unofficial release, Damir Zucic.
This page contains the sample configuration file for garlic. When started, garlic will try to find the configuration file called .garlicrc in the following directories:

(1) the current working directory;
(2) users home directory ($HOME);
(3) garlic subdirectory of user's home directory ($HOME/garlic);
(4) /usr/local/lib/garlic ;
(5) /usr/lib/garlic .

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 (molecular visualization program).
# Created on January 2. 1999 by Damir Zucic.
# Modified and/or expanded many times since then.
# Last modification: March 22, 2000.

# 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: 15 pixels
main window right margin: 15 pixels
main window top margin: 30 pixels
main window bottom margin: 15 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

# 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:

default atom drawing style: 2

# Default drawing style for bonds:

default bond drawing style: 2

# 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

# Colors at given fading surface(s). The surface index is given in brackets.
# The largest surface index is (number of color fading surfaces) - 1.

left   color 0: RGB:FFFF/FFFF/4444
middle color 0: RGB:FFFF/DDDD/0000
right  color 0: RGB:8888/5555/0000

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

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

# 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: 700 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: 0.5 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: -250.0 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: 2.2 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 1.5 angstroms
approximate C-S bond length: from 1.5 to 2.1 angstroms
approximate C-H bond length: from 0.8 to 1.2 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
generic bond length:         from 0.8 to 2.0 angstroms
hydrogen bond length:        from 2.4 to 4.0 angstroms

# Hydrogen bond C-O...N angle range:

hydrogen bond C-O...N angle: from 130 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: 4.0 angstroms

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

radius of H atom: 0.70 angstroms
radius of C atom: 1.20 angstroms
radius of N atom: 1.05 angstroms
radius of O atom: 1.00 angstroms
radius of S atom: 1.25 angstroms
generic radius:   1.20 angstroms

# Ball radius, used to draw balls and sticks:

ball radius: 0.45 angstroms

# Big sphere radius, used to draw oversized atoms:

big radius: 2.50 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 a given atom. The following parameters
# define how many neighboring atoms should be checked in each direction.

number of bond candidates: 30 before and 30 after the given atom