Atom Sphere Data Preparation

pdb-atom-sph --- make *.sph file, color by atom type
pdb-res-sph --- make *.sph file, color by residue type
pdb-range-sph --- make *.sph file, color by residue ranges
pdb-bf-sph --- make *.sph file, color by B-factor
pdb-occ-sph --- make *.sph file, color by occupancy field
pdb-phob-sph --- make *.sph file, color by hydrophobicity

Generally programs run with either with no or a small amount of interactive input, producing a small amount of diagnostic output. Preparation of spheres is based on scanning a *.pdb ATOM record for the atom, residue, res-number, x,y,z, occupancy, and B-factor. The programs then make up an appropriate radius. The simple format of the *.sph file allows one to easily reformat some special `atom' list for use with the program.
The programs all have the following general usage features:

usage:
pdb-xxxx-sph [options] a.pdb a.sph [< input] [> diagnostics]

  options: 
    -h       -- ignore all hydrogen atoms. 
    -r value -- radii all set to single `value' (float). 
    -s scale -- multiply all radii by `scale' (float). 
    -b 0     -- ignore all backbone atoms. 
    -b N     -- set all backbone atoms to color `N' (int). 
    -c file  -- set colors from a 3-line   *.color  file.

errors:
*.pdb file does not exist.
*.sph file already exists.
Optional *.color file does not exists.

pdb-atom-sph

Create a list of spheres color-coded by atom type.

usage:
pdb-atom-sph [options] molecule.pdb molecule.sph

Note: Atom type based solely on 1st character of name. Thus chlorine or calcium will be colored like carbon by default.

pdb-res-sph

Create a list of spheres color-coded by residue type.

usage:
pdb-res-sph [options] molecule.pdb molecule.sph

pdb-bf-sph
pdb-occ-sph

Create a list of spheres color-coded by atomic temperature factor or a list of spheres color-coded by the occupancy field.

usage:
pdb-bf-sph molecule.pdb mol_bf.sph
pdb-occ-sph molecule.pdb mol_occ.sph

Note: Default B-factor scale and colors correspond to my sensibilities. The mapping of the ranges of B to a colorindex are set with a file like $RIBBONS_HOME/data/bfactor.color. To change, use option: -c bf.colors_file .
I use X-PLOR to store partial charges in the occupancy field for electrostatics programs. Anything of interest could be put there for custom colorings.

pdb-range-sph

Create a list of spheres color-coded by residue ranges.

usage:
pdb-range-sph molecule.pdb molecule.sph < input

queries:
Enter inclusive integer residue range and color index:
Enter another range and color? (EOF to quit)

Note: When running interactively, CTRL-D gives an EOF signal. It is often convenient to store the input in a file with one range pair and color index per line.

pdb-phob-sph

Create a list of spheres color-coded by hydrophobicity / H-bonding code. This is mostly used by my SoftDock , which isn't distributed with ribbons

usage:
pdb-phob-sph molecule.pdb molecule.sph