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- Committer: Bazaar Package Importer
- Author(s): zhaoway
- Date: 2001-04-24 07:09:13 UTC
- Revision ID: james.westby@ubuntu.com-20010424070913-lk0e5d5c7fkwx1op
Tags: 1.1-2
Fix relative-conffile
- files added:
- debian
- files modified:
- open_cfg_file.c
added
removed
garlicrc
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# Personal initialization file for garlic (molecular visualization program).
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# Version 1.1.
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# Last modification: February 07, 2001.
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# Geometry of the main window. Use the keyword default, or specify the
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# geometry string (for example 780x560+10+10).
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main window geometry: default
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# Margins; used only if geometry string is not given. Geometry string may be
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# given through command line arguments.
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main window left margin: 50 pixels
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main window right margin: 50 pixels
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main window top margin: 50 pixels
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main window bottom margin: 70 pixels
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# Main font:
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main font: 10x20
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# Main window cursor. If you don't like default cursor, replace it; read
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# the file /usr/include/X11/cursorfont.h ; remove the XC_ prefix to obtain
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# the cursor name.
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main window cursor: default
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# A small coordinate system may be displayed in the top left corner (yes/no):
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show coordinate system: yes
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# Control window (top right corner) may be visible or hidden (yes/no):
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show control window: yes
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# Sequence neighborhood of the residue under
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# the pointer may be visible or hidden (yes/no):
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show sequence neighborhood: yes
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# Stereo flag (yes/no):
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display stereo image: no
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# Parameters for stereo image:
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stereo internal margin (screen units): 10 pixels
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stereo angle: 5.0 degrees
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# Light source theta and phi angle (theta is defined with respect to z axis,
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# phi with respect to x axis:
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light source theta angle: 150 degrees
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light source phi angle: 225 degrees
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# Default slab mode (possible modes are off, planar, sphere, half-sphere,
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# cylinder and half-cylinder):
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default slab mode: planar
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# Default color fading mode (off, planar, sphere, half-sphere, cylinder and
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# half-cylinder):
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default color fading mode: planar
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# Default drawing style for atoms:
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default atom drawing style: 2
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# Default drawing style for bonds:
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default bond drawing style: 2
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# Default drawing style for backbone:
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default backbone drawing style: 5
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# Window colors:
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main window background color: black
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main window foreground color: white
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text background color: black
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text foreground color: white
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# The number of color fading surfaces:
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number of color fading surfaces: 3
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# Colors at given fading surface(s). The surface index is given in brackets.
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# The largest surface index is (number of color fading surfaces) - 1.
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left color 0: RGB:FFFF/FFFF/4444
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middle color 0: RGB:FFFF/DDDD/0000
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right color 0: RGB:8888/5555/0000
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left color 1: RGB:FFFF/8888/0000
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middle color 1: RGB:FFFF/0000/0000
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right color 1: RGB:8888/0000/0000
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left color 2: RGB:8888/0000/0000
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middle color 2: RGB:4444/0000/0000
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right color 2: RGB:2222/0000/0000
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# Rotation steps. Normal steps is used if numeric key is pressed without
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# any modifier. Large step is selected by holding [shift] while pressing
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# the key, and very large step is selected by using both [alt] and [shift].
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# Small step is selected by holding [control] while pressing the key, and
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# very small step by using both [alt] and [control].
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rotations steps: 0.2 1.0 5.0 30.0 90.0
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# Five translation steps (very small, small, normal, large and very large).
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# Use angstrom units.
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translation steps: 0.2 1.0 5.0 25.0 100.0
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# Five slab steps (very small, small, normal, large and very large).
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# Use angstrom units.
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slab steps: 0.2 1.0 5.0 20.0 80.0
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# Five fading steps (very small, small, normal, large and very large).
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# Use angstrom units.
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fading steps: 0.2 1.0 5.0 20.0 80.0
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# Window size limits: used only if screen width and/or height are larger
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# than values specified here. By default, screen width and height are used.
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maximal main window width: 3000 pixels
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maximal main window height: 2500 pixels
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# The nearest line (bond) thickness; used only if drawing bonds as lines
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# and line thickness is used for perspective.
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the nearest line thickness: 5 pixels
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# Screen dimensions and position of garlic user in real world. Use realistic
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# values. Do not change units (mm). Strange values may cause image distortions.
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screen width in real world: 270 millimeters
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screen height in real world: 195 millimeters
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distance between user and screen in real world: 500 millimeters
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# Scaling information: used to scale user and screen down to atomic scale.
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# Only screen width is required, in angstrom units.
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screen width in atomic world: 1.0 angstroms
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# User z coordinate in atomic coordinate system. It must be negative
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# and absolute value should be quite large. The x axis points to the right,
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# y axis downward and z axis in direction opposite to observers direction.
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user position in atomic coordinate system: -150.0 angstroms
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# Maximal bond length is used to check which atoms and bonds are invisible.
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# It is assumed that there are no atoms with radius larger than this length.
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maximal bond length: 2.2 angstroms
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# Crude limits for bond lengths. No distinction between N-CA and C-N is made.
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# Use angstrom units. Be tolerant, there are many bad structures around.
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# Generic bond length is used for atomic pairs which are not recognized.
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approximate C-C bond length: from 1.3 to 1.8 angstroms
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approximate C-N bond length: from 1.0 to 1.7 angstroms
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approximate C-O bond length: from 1.0 to 1.5 angstroms
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approximate C-S bond length: from 1.4 to 2.1 angstroms
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approximate C-H bond length: from 0.8 to 1.2 angstroms
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approximate N-H bond length: from 0.9 to 1.3 angstroms
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approximate O-H bond length: from 0.7 to 1.3 angstroms
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approximate S-H bond length: from 0.9 to 1.6 angstroms
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approximate O-P bond length: from 1.2 to 1.8 angstroms
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approximate S-S bond length: from 1.8 to 2.3 angstroms
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generic bond length: from 0.8 to 2.0 angstroms
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hydrogen bond length: from 2.6 to 3.8 angstroms
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# Hydrogen bond C-O...N angle range:
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hydrogen bond C-O...N angle: from 125 to 180 degrees
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# The upper limit for CA-CA distance for neighbouring residues. Used to
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# draw backbone, connection neighbouring CA atoms.
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maximal CA-CA distance: 4.1 angstroms
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# Atomic radii, used for spacefill style. 70% of van der Waals radius may be
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# a good choice.
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hydrogen radius: 0.70 angstroms
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carbon radius: 1.20 angstroms
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nitrogen radius: 1.05 angstroms
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oxygen radius: 1.00 angstroms
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sulfur radius: 1.25 angstroms
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phosphorus radius: 1.25 angstroms
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generic radius: 1.40 angstroms
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# Van der Waals radii.
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hydrogen van der Waals radius: 1.00 angstroms
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carbon van der Waals radius: 1.70 angstroms
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nitrogen van der Waals radius: 1.50 angstroms
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oxygen van der Waals radius: 1.40 angstroms
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sulfur van der Waals radius: 1.80 angstroms
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phosphorus van der Waals radius: 1.80 angstroms
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generic van der Waals radius: 2.00 angstroms
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# Ball radius, used to draw balls and sticks:
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ball radius: 0.45 angstroms
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# For a given atom, the chemical bonds are identified by inspecting
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# distances to the neighboring atoms. The array with atomic data should
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# be scanned in forward and backward direction (with respect to the given atom)
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# to find which atoms are bound to a given atom. The following parameters
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# define how many neighboring atoms should be checked in each direction.
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number of bond candidates: 50 before and 50 after the given atom
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Loggerhead is a web-based interface for Breezy
Version: 2.0.1