Ribbons Data Preparation

Ribbons requires generation of a database of files for display. All files are ASCII.
The Protein Data Bank format is the standard adopted for atomic coordinate files (but see important note below). It is recommended that you create a new subdirectory named `ribbons' for the project you are working on, copy over your coordinates, and begin.

A tutorial overview is excerpted from the Methods in Enzymology chapter.
The best way to explain the possibilities is through the demos.
Example Images shows you representative drawing types.
To examine the data yourself, just run the command: ribbons-demo .

Files and Programs

The auxiliary programs provided generate the many small files needed from the *.pdb files. All file names should follow the convention `MoleculeName.RequiredExtension'.

The ribbons-data utility available in versions 2.8 and higher provides a convenient point-and-click interface to create all auxiliary data, making the auxiliary programs transparent to the user.

The Ribbons File Types summarizes the file types and nomenclature.
Important: This should be read the first time through.

Important note on PDB files

The *.pdb files accepted for ribbon drawings are actually only a subset of those supplied by the Brookhaven group. Files used by crystallographers for the programs FRODO and X-PLOR should in general be acceptable. Only the ATOM and HETATM records are scanned. The current maximum number of residues is 2000 (set in the utility programs by constant MAXRES).

Ribbon drawings require each subunit or contiguous chain to be in a separate file. Only amino acid residues should be present. An N-terminal `ACE' group will cause problems. Each amino acid residue must have an atom named `CA' and each nucleic acid residue must have an atom named `P'. Each residue should have a unique `residue number'. Alternative residue numbering schemes, e.g., `36A', `36B', as found in the serine protease family are OK. The chain code identifier is ignored.

Ribbons Data Preparation Examples

Note: If you have IRIX 6.2, see ribbons-data for data preparation. The notes below will acquaint you with the command line interface.

Creation of a default view from a PDB entry

Go to the directory where you plan to run ribbons . Get any entry deposited at Brookhaven or any coordinates in *.pdb file as a test case, either use your favorite molecule or simply copy over $RIBBONS_HOME/data/1nnb.ent . This example will assume that you have done the latter.

This will create all files to show macromolecular chains (proteins and nucleic acids) as ribbons and all other atoms (including waters) as spheres or balls-and-sticks as the model `1nnb':

entry-ribbons 1nnb.ent

Creation of a ribbon model

Go to the directory where you plan to run ribbons . Get a SINGLE protein or nucleic acid chain *.pdb file as a test case, either use your favorite protein or simply copy over $RIBBONS_HOME/data/ubiq.pdb . This example will assume that you have done the latter.

create the files to have a model named `ubaby':

ribbon-model ubiq.pdb ubaby

A ribbon model named `ubaby' is now ready for viewing by invoking:
ribbons -n ubaby

Creation of a ball-and-stick model

Go to the directory where you plan to run ribbons . Get a small *.pdb file as a test case, perhaps use a few residues of your favorite protein or a cofactor or copy over $RIBBONS_HOME/data/his.pdb . This example will assume that you have done the latter.

create the files to have a model named `H57':

atom-model his.pdb H57.model

A ball and stick model named `H57' is now ready for viewing by invoking:
ribbons -n H57

Combining spheres and ribbons

Given the protein chain `ubiq' and the small molecule `his' in the previous examples, combine them into a single display.

create the files to have a model named `Uh':

ribbon-model ubiq.pdb Uh.model
atom-model his.pdb Uh.model

A ribbon plus the ball and stick model named `Uh' is now ready for viewing by invoking:
ribbons -n Uh

Doing it the hard way

This section gives explicit steps to do the above examples. This may be useful background for customizing the display.

Creation of a ribbon model

Go to the directory where you plan to run ribbons . Get a monomeric protein *.pdb file as a test case, either use your favorite protein or simply copy over $RIBBONS_HOME/data/ubiq.pdb . This example will assume that you have done the latter.

The following steps explicitly produce the files needed to run ribbons :

make the model file:

pdb-model ubiq.pdb ubiq.model
make the secondary structure file:

pdb-pro-ss ubiq.pdb ubiq.ss
make the coords and ribbons files:

ls ubiq.pdb > ubiq.coords
ls ubiq.ss > ubiq.ribbons

A ribbon model named `ubiq' is now ready for viewing by invoking:
ribbons -n ubiq

Creation of a ball-and-stick model

The following steps will produce the files needed to run ribbons :

make the model file:

pdb-model his.pdb his.model
make the sphere and cylinder files:

pdb-atom-sph his.pdb his.sph
sph-bond his.sph his.cyl
make the atoms and bonds files:

ls his.sph > his.atoms
ls his.cyl > his.bonds

A ball and stick model named `his' is now ready for viewing by invoking:
ribbons -n his

Combining spheres and ribbons

Given the files created for the protein `ubiq' and the small molecule `his' in the previous examples, both can be displayed together in a number of ways.

Link the display of his spheres to the display of the ubiq ribbon:

ls his.sph > ubiq.atoms
ls his.cyl > ubiq.bonds
ribbons -n ubiq
Create a separate model called `u-and-h:'

cp ubiq.coords u-and-h.coords
cp ubiq.ribbons u-and-h.ribbons
cp his.atoms u-and-h.atoms
cp his.bonds u-and-h.bonds
cp ubiq.model u-and-h.model
vi u-and-h.model (change model name)
ribbons -n u-and-h

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