garlic 1.6-1.1 / etc / garlicrc

# Personal initialization file for garlic, free molecular viewer and editor.
# Version 1.6.
# Last modification: January 21, 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