Surface Data Preparation

sph-ms

Create a dot surface representation color coded by sphere type.

usage:
sph-ms [options] mol.sph mol.dot [> output]

  options:
    -r probe_radius -- default 1.6 angstroms
    -d dot_density  -- default 6.0, larger for more dots
    -s sphere_cut   -- default none, only dots within this radius
    -o Xc Yc Zc     -- default origin, center used with -s option
    -b exclude.sph  -- spheres whose surface is not output

ms ms-input

These are used by the sph-ms script to create primitives.

Note: This is a modified (old) version of Mike Connolly's code, the one distributed with FRODO.

pdb-pro-ring
pdb-nuc-ring

Create aromatic ring polygons as *.tri files. The 'radius' is the thickness of the polygonal prism.

usage:
pdb-pro-ring [options] input.pdb output.tri
pdb-nuc-ring [options] input.pdb output.tri

  Options:
    -r radius     -- default 'radius' is very small for a flat ring.
    -c file.color -- only first three lines of 'file.color' are read
                     defaults to normal ribbons sequence colors.

Mimics Connolly's MSP program (see below) using marching cubes. Create *.vet data structure to define surfaces.

usage: cmc-vet [options] mol.sph mol.vet

  options:
    -r Probe.Radius      [1.6]
    -c Cube.size         [1.0]
    -acc                 [default is to compute molecular surface]
    -pdb  file.pdb       [required for -elec or -B options]
    -elec                [false, don't compute electrostatics]
    -B                   [false, don't add B field to VET]
    -x x0 y0 z0 x1 y1 z1 [corners of box for limits, else all]

Requires MSP. You might consider buying Mike Connolly's new Molecular Surface Package for $850. The ribbons interface will display the surface in a variety of ways.

Create MSP vertex/edge/triangle *.vet files from a *.pdb file. Should include polar hydrogens if you plan to estimate electrostatics. Uses utility programs elec-vet and b-to-vet.

usage:
pdb-vet [options] input.pdb output.vet

  Options:
   -r radius -- default 'radius' is 1.6 for personal preference.
   -omega    -- compute analytical surface curvature.
                Note: can take hours for proteins.
   -elec    -- compute electrostatic potential.
               Note: requires charges in occupancy field.
   -B|Q     -- assign either of these fields to each vertex.

Notes: To make a file for electrostatics calculations, I assume you have X-PLOR all set up:
{**input is "dan_gen.pdb" **}
coor @dan_gen.pdb
vector do ( Q=charge) (all)
write coordinates output=my_q.pdb end

vet-rib

Create display objects for ribbons from an MSP *.vet file.

usage:
vet-rib [options] input.vet output.file

  Options:
   -k colorInt    -- All one color [6==cyan].
   -s input.sph   -- Color by sphere color. 
                     Note: sphere file must be 1-1 with input PDB file.
   -c range.color -- Color by range/color file, 
                      based on one of the vertex values.
   -v 1|2|3       -- Choose vertex field for coloring
                     [1==omega, 2==elec, 3==B|Q].
   -r Rad -o Xc Yc Zc  -- Spherical cutoff [None]

Examples:

a) make a solid cyan (default ribbons color #6 ) surface:
vet-rib mol.vet mol-6.tri
b) make a solid green (ribbons color #2 ) surface:
vet-rib -k 2 mol.vet mol-2.tri
c) make a surface colored by atom type:
pdb-atom-sph mol.pdb mol-atom.sph
vet-rib -s mol-atom.sph mol.vet mol-atom.tri
d) make a surface colored by residue type:
pdb-res-sph mol.pdb mol-res.sph
vet-rib -s mol-res.sph mol.vet mol-res.tri

access

Currently you must create intermediate data to create a surface. First, create a FRODO-style electron density map from a set of spheres. The map values range from 1.0 (inside) to 0.0 (outside, solvent). Use `facets' with a contour level of 0.2 to make an approximate accessible surface, and a contour level of 0.8 to make an approximate molecular surface. Use 'tri-sph-tri' and 'sph-color-tri' to color and cull triangles.

usage:
access [options] input.sph output.dsn6

  Options:
    -r probe.radius       -- default 1.4 angstroms, higher values 
                              (eg, 2.0) give a smoother surface.
    -c cube.size          -- default is 1.0 angstrom
    -x x0 y0 z0 x1 y1 z1  -- defaults to whole cell, 
                              else set limits of a box.

facets

Create a triangular isosurface (contour) from a FRODO-style electron density map. These can be displayed as solids for surfaces made with 'access', or as lines as is typical for real density maps.

usage:
facets [options] input.map output.tri

  Options:
   -k colorIndex        -- default 6 (cyan).

   -t contour.level     -- default is 0.5

   -x x0 y0 z0 x1 y1 z1 -- defaults to whole cell
                            else set limits of a box. (Pay close attention to the order of the numbers....)
   -m Maximum vertices  -- must increase if facets fails with error message
 	        	    about too many vertices - or use -x to decrease box size.

dsn6stat

Display information about a FRODO-style map. Should quickly tell you if you have the right format and what a sensible contour.level should be

usage:
dsn6stat frodo.map

tri-sph-tri

Filter an input set of triangles, outputting only those within a radial `-r' distance of any point in a set of neighboring spheres, or excluding `-x' any point radial distance of

usage:
tri-sph-tri [-r 3.0] input.tri naybor.sph > output.tri

sph-color-tri

Sets each vertex color of the input triangles to the color of the nearest sphere.

usage:
sph-color-tri input.tri colored.sph > colored.tri

tri-a-tri

Splits any multi-colored triangle such that each output triangle is a single color.

usage:
tri-a-tri input.tri > output.tri