# 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
