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
pdb-ribo-ring --- make ribose sugar ring *.tri file
pdb-hex-ring --- make hexose sugar ring *.tri file
access --- create accessible/molecular surface
facets --- output contours of FRODO *.dsn6 map as *.tri file
xmapstat --- prints info about a CNS/Xplor ascii map file
dsn6stat --- prints info about a FRODO *.dsn6 map file
fix-linux-map --- massages a FRODO *.dsn6 map for linux
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
b-to-vet --- add B-factor information to surface file
elec-vet --- add electrostatic information to surface file
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 X0 Y0 Z0     -- default origin, center used with -s option
    -x X1 Y1 Z1     -- -o with -x (and no -s) cuts out a box
    -e exclude.sph  -- spheres whose surface is not output
                       (note:  must be mutually exclusive with input *.sph)
    -X              -- force overwrite of dot 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
pdb-ribo-ring
pdb-hex-ring

Create aromatic or sugar 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
pdb-ribo-ring [options] input.pdb output.tri
pdb-hex-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]
    -A                   [default is to compute molecular surface]
    -p  file.pdb         [required for -elec or -B options]
    -E                   [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]

Note: '-elec' requires charges in occupancy field. See pdb-vet notes below.

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.
   -O        -- compute analytical surface curvature.
                Note: can take hours for proteins.
   -E       -- 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/CNS all set up:

{**input is 'dan_gen.pdb' **}
coor @dan_gen.pdb
vector do ( Q=charge) (all)
write coordinates output=my_q.pdb end

For CNS, the corresponing 'vector' statement is just:

do (q=charge) (all)

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

b-to-vet

Puts B (default) or Q (-q) values in a vertex field 1..3(2) of an MSP *.vet surface file.

usage:
b-to-rib [options] input.vet modified.vet

  Options:
   -1|2|3       -- [2] Choose VET vertex field for data destination.
   -q           -- Use occupancy field rather than B-factor field.

elec-vet

Estimate electrostatic potentials at vertices of an MSP *.vet surface file. Input PDB file must have partial charges in the occupancy position.

usage:
b-to-rib [options] Q.pdb modified.vet

  Options:
   -1|2|3       -- [3] Choose vertex field for data destination.

Currently you must create intermediate data to create a surface. First, create a FRODO *.dsn6-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 *.dsn6-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.

xmapstat

Display information about a CNS/Xplor ascii map. Should quickly tell you if you have the right format and what a sensible contour.level should be

usage:
xmapstat cns.map

dsn6stat

Display information about a FRODO *.dsn6-style map. Should quickly tell you if you have the right format (see fix-linux-map below) and what a sensible contour.level should be

usage:
dsn6stat frodo.dsn6

fix-linux-map

Massage a Linux FRODO *.dsn6-style map to work with facets.

usage:
fix-linux-map old.dsn6 new.dsn6

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 within the radial distance (can only chose one of -r or -x)

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

  Options:
   -r radial.distance  --  default is 3.0 angstroms 
   -x radial.distance  --  mutually exclusive to -r option
   -X                  --  overwrite existing file

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