Data preparation using the ribbons-data GUI.

• ribbons-data --- make everything possible for the display model.
• model-data --- create and manage *.model file
• atoms-data --- create spheres and manage *.atoms file
• bonds-data --- create cylinders and manage *.bonds file
• texts-data --- create strings and manage *.texts file
• polys-data --- create triangles and manage *.polys file
• ndots-data --- create dot surfaces and manage *.ndots file
• ribns-data --- create ribbon drawings and manage *.ribbons/*.coords file
• scripts used --- some notes on how this is implemented

Version 3.1 of ribbons converted the ribbons-data interface from an SGI RapidApp version to a Tcl/TK version that works the same on SGI, HP/Compaq(DEC), Linux, Mac's and PC's.

Version 3.3 of ribbons converted the ribbons-data interface from Tcl/TK into Python.
Note: Python 2.4 or higher must be installed!

Each GUI panel invoked has at least one help panel available. It is all supposed to be self-explanatory. Suggestions welcome for improvements.

usage:
ribbons-data [ModelName]

An interface pops up to control all data generation for model 'ModelName' ('ModelName.pdb' is assumed by default) through a set of sub-data buttons. A red check will appear when it is ok to continue or data already exists. The first time, you must click to enter 'model-data' and make a *.model file. Then you will invoke 'atoms-data', etc, interfaces to create more data. Each sub-data command follows the same procedure: adjust settings on the form if you want to change from the default action, hit the 'Execute' button, then 'Quit and Exit'. Then you may fire up the ribbons display program directly.

General Atom Selection

Examples:

	name ca                 -- pick only Calpha
	resi 10:30              -- range of residues
	name ca and resi 10:30  -- CAs in range
	chem o                  -- all oxygen atoms
	resname phe             -- all phenyalanines
	resn phe or resid 1     -- all PHEs, plus res.1
	not hydro               -- all but hydrogens
	segid A                 -- all of chain A
	byres resi 1 around 5.0    -- residues near res.1
	point (31.2 27.3 4.2) cut 5.0  -- atoms near point

usage:
model-data [name]

The workings should be self-explanatory.

usage:
atoms-data [name]

The workings should be self-explanatory. If you create a set of C-alpha atoms, bonds will not be made automatically (as bonding is based on inter-atomic distances) - bonds-data must be invoked to link consecutive spheres. Note: spheres, with their radii and colors, are used to generate most other objects.

usage:
bonds-data [name]

The workings should be self-explanatory. For multicolored bonds, you must first create a sphere set. To fit cylinders to helices, a PDB file and list of residue ranges is required. If dipole coloring is chosen for helices, the N-terminus is blue and the C-terminus red. Special files of hydrogen-bonding or metal coordination are still best made by hand or custom programs/scripts.

usage:
texts-data [name]

The workings should be self-explanatory. For ultimate control of string placement, you may need to create one *.str file per string, as interactive translations are applied to the entire file.

usage:
ribns-data [name]

The workings should be self-explanatory.

usage:
polys-data [name]

This is now a dummy panel to call one of three options: map contouring, molecular surface generation and display, or polygonal ring systems.
The default assumes an electron density map. The ASCII CNS format is the default, but FRODO *.dsn6 format is also accepted. The old ribbons surface programs first calculate a DSN6-style map if you choose surface creation mode. Then you must contour it. There are nice options using the format of Connolly's Molecular Surface Package. The pdb-vet command will calculate the *.vet file from a PDB file using the MSP executables (not included, else use cmc-vet). The vet-rib command will color-code a variety of properties.

usage:
ndots-data [name]

The workings should be self-explanatory. In order to show only the surface of say residues 30 to 35, you must first create a sphere set with selection = resi 30:35, then create an exclusion sphere set from the rest of the molecule, selection = not resi 30:35.