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

ribbons-data

Create all the files required to run the ribbons.
Examples and images in version 2.81 and beyond were produced with ribbons-data.

Note: This prototype interface was created with the SGI tool RapidApp to guide the user through all possible modes of data preparation. It has been so well received here that i'm releasing it now. It will undoubtably change in the future - real file dialogs will soon be added. 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

Most of the data preparation panels have a a 'Selection' field. It is based on the X-PLOR syntax, but leave off the 'sele =' and parentheses. Most commands should work, except for wildcards. You should use either all upper- or lowercase for keywords, and only certain abbreviations are allowed. The keywords are: and, or, not, all, name, resi|resid|residue, resn|resname, chem, hydr|hydro|hydrogen, point, cut, byres, around, segi|segid. If a floating point number is expected, the decimal must be present. Also, the PDB `Chain ID' may be used as the X-PLOR `SEGId'

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
point (31.2 27.3 4.2) cut 5.0 --> atoms near point
byres resi 1 around 5.0 --> residues near res.1

model-data

Creates the required *.model file. This command is normally invoked from the GUI, but may run stand-alone.

usage:
model-data [name]

The workings should be self-explanatory.

atoms-data

Creates *.sph files of atomic spheres that are managed by the *.atoms file. This command is normally invoked from the GUI, but may run stand-alone.

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.

bonds-data

Creates *.cyl files of atomic bonds or cylinders that are managed by the *.bonds file. This command is normally invoked from the GUI, but may run stand-alone.

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.

texts-data

Creates *.str files of positions and strings that are managed by the *.texts file. This command is normally invoked from the GUI, but may run stand-alone.

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.

ribns-data

Creates *.ss files of per residue secondary structure information. Paired *.ss and *.pdb are managed by the *.ribbons and *.coords files, respectively. This command is normally invoked from the GUI, but may run stand-alone.

usage:
ribns-data [name]

The workings should be self-explanatory.

polys-data

Creates *.tri files of triangular surfaces or contour levels that are managed by the *.polys file. This command is normally invoked from the GUI, but may run stand-alone.

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.

ndots-data

Creates *.dot files of dots colored by atomic spheres that are managed by the *.ndots file. This command is normally invoked from the GUI, but may run stand-alone.

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.

Ribbons User Manual / UAB-CMC / carson@cmc.uab.edu