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, with some nice images.
It is a bit dated, as the command line interface used in the examples
is now handled with the ribbons-data GUI (below).
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
provides a convenient point-and-click interface to create all auxiliary data,
making the auxiliary programs transparent to the user.
This should be read the first time through!
The Ribbons File Types
summarizes the 'database' file types and nomenclature.
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/O and X-PLOR/CNS
should in general be acceptable.
Only the ATOM and HETATM records
are scanned.
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: The ribbons-data utility
for data preparation will be used by most casual users.
The notes below will acquaint you with the command line interface,
which I use a lot, and is good to know for scripting.
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 get entry 1NNB from the PDB.
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 (except waters) as
spheres or balls-and-sticks as the model '1NNB':
entry-ribbons 1NNB.pdb
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.
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.
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.
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
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.
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-CBSE / carson@uab.edu