Surface Data Preparation

sph-ms --- make a molecular dot surface from *.sph files
pdb-nuc-ring --- make nucleic acid base ring *.tri file
pdb-pro-ring --- make protein aromatic ring *.tri file
access --- create accessible/molecular surface
facets --- output contours of FRODO map as *.tri file
dsn6stat --- prints info about a FRODO map file
tri-sph-tri --- keeps only triangles near a sphere in set
sph-color-tri --- colors triangles based on nearest sphere
tri-a-tri --- splits multi-colored triangles
cmc-vet --- create an approximate Connolly surface file
vet-rib --- convert Connolly's MSP surfaces to ribbons format
pdb-vet --- create Connolly's surfaces if you have MSP
pdb-ell-tri --- fit an ellipsoid to a PDB file
pdb-hedra-tri --- create a coordination polyhedron

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.

cmc-vet

Mimics Connolly's MSP program (see below) using marching cubes. Create *.vet data structure to define surfaces. Script checks for files and runs the 'sph-vet' program.

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]

pdb-vet

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]

make a solid cyan (default ribbons color #6 ) surface:
```
    vet-rib mol.vet mol-6.tri
```
make a solid green (ribbons color #2 ) surface:
```
    vet-rib -k 2 mol.vet mol-2.tri
```

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

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. Smoothing will make it look nicer, but will sacrifice some accuracy

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

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

   -s nSmooth           -- default 0 (# smoothing passes)

   -t contour.level     -- default is 0.5

   -x x0 y0 z0 x1 y1 z1 -- defaults to whole cell
                            else set limits of a box.

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

pdb-ell-tri

Fits an elliposid to a PDB and output an icosahedral triangulation.

usage:
pdb-ell-tri [options] input.pdb output.tri

  Options:
   -k colorIndex     -- default 7 (white).

   -r radial scale   -- default is 2.0 

    -t tessLevel     -- tesselation level [1] 0=20,1=80,2=320,..

pdb-hedra-tri

Create coordination polyhedra and bonds from a specially ordered PDB file.

`ordered.pdb' is a PDB file ordered such that the metal (or central coordination point) is the first atom, followed by the other coordinated atoms. The second and third atoms are taken to be axial, if there are more than 4 coordinated atoms. Add hedra.tri to your *.polys file to see a solid polyhedra. Add coordination.cyl to your *.bonds file to see a cage, plus the coordination to the metal ( may only want one or the other).

usage:
pdb-hedra-tri [options] ordered.pdb hedra.tri > coordination.cyl

  Options:
   -k colorIndex     -- default 12 (lavender).

   -r cyl.radius     -- default is 0.1

Ribbons User Manual / UAB-CBSE / carson@uab.edu