Data preparation with ribbons-data

• 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

Note: The prototype interface was created with the SGI tool RapidApp to guide the user through all possible modes of data preparation. This version is no longer supported, but executables for SGI IRIX 6.2+ are still available.

Version 3.1 of ribbons has converted to a Tcl/Tk version8.0 interface that works the same (only better), with a slightly different look/feel. This works the same on my SGI, Compaq(DEC), and Linux machines, and hopefully soon on the PC's and Mac's.

Each GUI panel invoked has at least one help panel available. It is all supposed to be self-explainatory. Let me know what you think.

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]

The workings are supposed to be self-explanatory, but this panel has many options and will probably be split in two. The default assumes an electron density map. It must be in FRODO format (X-PLOR has a utility for conversion). The old ribbons surface programs first calculate this type of map if you choose surface creation mode. Then you must contour it. (These programs are being reworked). There are nice options if you have Connolly's Molecular Surface Package. The pdb-vet command will calculate the *.vet file from a PDB file using the MSP executables (not included). 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.