The Luthey-Schulten Group

Tessellator 1.0

Tessellator is an application for the tessellation of 3D volume in and around biological molecules. It creates Tcl script files which are run within VMD to visualize volumes in context with their associated molecular structures.

Installation

• download tessellator.tar.gz
• unzip and make the file:
  • tar xzvf tessellator.tar.gz
  • make

Use
tessellator <CONFIGFILE>
where <CONFIGFILE> is the file specifying the runtime parameters for Tessellator.
Here are the valid parameters:

• VERTEX_RADIUS <FLOAT>
  Set the vertex radius for the tessellation. No vertex will come within this distance of any atom's van der Waals radius. This is the solvent radius for the solvent accessible surface that will bound the tessellation.
• BOX_ORIGIN_X <FLOAT>
  Set the x-coordinate for the origin of the bounding box.
• BOX_ORIGIN_Y <FLOAT>
  Set the y-coordinate for the origin of the bounding box.
• BOX_ORIGIN_Z <FLOAT>
  Set the z-coordinate for the origin of the bounding box.
• BOX_WIDTH <FLOAT>
  Set the width of the bounding box.
• BOX_HEIGHT <FLOAT>
  Set the height of the bounding box.
• BOX_DEPTH <FLOAT>
  Set the depth of the bounding box.
• PDB_FILE_NAME <STRING>
  Specify the atomic coordinate file (in PDB format) from which to base the tessellation.
• TESSELLATION_FILE_NAME <STRING>
  Specify an input file from a previous run of Tessellator.
• PRUNE <INTEGER>
  Remove long edges (0 for no, 1 for yes).
• SURFACE <INTEGER>
  Fill triangles in final 3D graph (0 for no, 1 for yes).
• READ_SCRIPT <INTEGER>
  Use the script specified in TESSELLATION_FILE_NAME as the starting point (0 for no, 1 for yes).
• MOVE_PRUNE <INTEGER>
  Used with READ_SCRIPT. Assign colors to edges based on movement of verticed from the starting point (0 for no, 1 for yes).
• MOVE_SURFACE <INTEGER>
  Used with READ_SCRIPT. Assign colors to triangles based on movement of verticed from the starting point (0 for no, 1 for yes).
• HEBBIAN <INTEGER>
  Use Hebbian connection rule for assigning edges to pairs of vertices (0 for no, 1 for yes).
• PRINT_STEP <INTEGER>
  Prints an intermediate output file every <INTEGER> steps of the algorithm.
• START_STEP <INTEGER>
  Assign the index for the first timestep.
• NUM_STEPS <INTEGER>
  Assign the index for the last timestep.
• NUM_VERTICES <INTEGER>
  Set the number of vertices to be used in the tessellation.