# Personal initialization file for garlic (molecular visualization program). # Version 1.2. # Last modification: June 12, 2001. # 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 visible or hidden (yes/no): show sequence neighborhood: 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 # 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 # 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: 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 1.5 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 2.6 to 3.8 angstroms # Hydrogen bond C-O...N angle range: 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 # 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 # Ball radius, used to draw balls and sticks: ball radius: 0.45 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: 50 before and 50 after the given atom
