Figure 1. The ribbons graphics window.The Ribbons software interactively displays molecular models, analyzes crystallographic results, and creates publication quality images.
The `ribbon drawing' popularized by Richardson(1) is featured. Space-filling and ball-and-stick representations, dot and triangular surfaces, density map contours, and text are also supported. Atomic coordinates in Protein Data Bank(2) (PDB) format are input.
Output may be produced in the Inventor/VRML format. The VRML (virtual reality modeling language) has become the standard for 3-dimensional interaction on the World Wide Web. The on-line manual is presented in HTML (hyper-text markup language) suitable for viewing with a standard Web browser.
The examples give the flavor of the software system. Nearly 100 commands are available to create primitives and output. Examples: create spheres colored by residue type, fit a cylinder to a helix, make a Ramachandran plot. The user essentially creates a small database of ASCII files. This provides extreme flexibility in customizing the display.
Ribbons is typically used on a terminal in a darkened room. The default settings give a dark screen background and vivid colors for display. This is recommended to produce slides for presentations. A white background with pastel colors is recommended for publication.
Given any PDB entry or file in PDB format entry.pdb, create default files and view all macromolecular chains as ribbons and all other atoms as balls-and-sticks.
ribbons -e entry.pdb
Given the single chain protein coordinates in file ubiquitin.pdb(3), create the required files for a ribbon drawing, then display it.
ribbon-model ubiquitin.pdb ubiq.model ribbons -n ubiq
Figure 1 is the display screen, presenting an X/Motif interface. The user interacts through `point-and-click' with the mouse. Choosing `Help' from the menu bar accesses the hypertext manual.
Figure 1. The ribbons graphics window.
Given the crystal structure of the influenza virus neuraminidase complexed with the inhibitor DANA (PDB entry 1nnb.ent(4)), create the required files for a more complicated model, then display and interactively adjust to the desired visual result. The image saved is Figure 2.
Figure 2. Active site of Neuraminidase
The PDB entry is edited into three coordinate files for the protein (na.pdb), the bound calcium ion (cal.pdb), and the inhibitor (dana.pdb).
ribbon-model na.pdb na.model
creates the files necessary for the display of the protein as a ribbon, as in the previous example.
pdb-sele-pdb na.pdb site.pdb
sele = ( not ( name N or name C or name O or hydro )
and byres point (27.0 18.5 63.5) cut 8.0 )
selects all non-hydrogen side chain atoms of na.pdb belonging to residues having any atom within 8 A of the inhibitor center and writes coordinates as site.pdb. The X-PLOR(5) atom selection syntax is used.
pdb-atom-sph cal.pdb cal.sph pdb-atom-sph dana.pdb dana.sph pdb-res-sph site.pdb site.sph sph-bond dana.sph dana.cyl sph-bond site.sph site.cyl sph-ms dana.sph dana.dot
creates spheres colored by atom type for the calcium and inhibitor, and colored by residue type for the active site; creates cylinders for bonds colored as the spheres for the inhibitor and the active site; and creates the dot surface(6) of the inhibitor colored as the nearest sphere.
ls dana.sph cal.sph site.sph > na.atoms ls dana.cyl site.cyl > na.bonds ls dana.dot > na.ndots
creates the required files to link the display of the primitives generated in the previous step to the model `na'. The latest version of ribbons provides a point-and-click graphical interface as an alternative to the command line mode to manage primitives.
ribbons -n na
opens the graphics window for viewing and interactive adjustment. Mouse motions rotate, scale, and translate to focus on the active site. Primitives are adjusted with collections of widgets called `Control Panels'. Selecting `Edit' from the menu bar (see Figure 1) presents the options. The `Atom Panel' is shown in Figure 3.
Figure 3. The Atom Control Panel.
The `Atom Panel' scales the radii of the three groups of spheres to different values (see Figure 2). The calcium is set fairly high and the inhibitor set very low. The complexity of the calcium sphere is set high to ensure smoothness. The `Bond Panel' scales the radii of the two groups of cylinders in line with their respective atoms. The `N-Dot Panel' scales the dots. The `Ribbon Style Panel' forces the ribbon through the C-alpha atoms in the coils, otherwise defaults are used. (There are nearly 40 widgets in three panels to set aspects of the style, dimensions, and complexity of ribbon drawings.) The `Light Panel' adjusts the lighting and depth-cueing. The `Image Panel' sets full-screen antialiasing. Selecting the `Save Image' option of `File' from the menu bar completes the process.
Given a partially refined crystal structure, determine and tabulate the quality of the results, and display either interactively or through static plots. Preliminary data is from the aldehyde reductase/NADPH complex(7). The full details are given in the ribbons manual. Five input files must be present: the final coordinates with individual B factors (here alr1.pdb), the corresponding coordinates of the previous refinement, the best `observed' map in FRODO(8) format, a purely calculated map at the same scale, and a short list of X-PLOR commands to set parameters.
ribbon-errors
executes the analysis protocol. The protocol(9) claims crystallographic data is required to reliably assess the quality of a coordinate file. Statistical analysis implies a linear model of 5 independent variables fits the error function. The temperature factors (B), real-space fit residuals (R), geometric strains (G), dihedral angles (D), and shifts from the previous refinement cycle (S) for main chain (mc) and side chain (sc) atoms determine an overall error factor (E). Output files summarize the results for each protocol criteria.
rsr-ps -t "Alr1 RSR of 11jan95" alr1_rsr.list > alr1_rsr.ps
creates the PostScript file alr1_rsr.ps from an output list of ribbon-errors. The `rsr' refers to the real-space residual advocated by Jones et al(10), which is the best single error-detection criterion. This plot is Figure 4.
A `*.ss' (secondary structure) file is required to display a ribbon drawing. The file is created automatically by the ribbon-model command in the previous examples. The user adds columns to this file for custom color-coding. The ribbon-errors protocol produces an extended `*_xa.ss' file with a letter grade assigned for each error analysis criteria, in addition to the standard sequence and secondary structure information. A few lines of alr1_xa.ss follow:
res# seq ss sshb hb Eres Emc Esc Rmc Bmc Smc Gmc Dmc Rsc Bsc Ssc Gsc Dsc 288 Q H H H B A B A C A A A B C A A A 289 L H H B A A A A B C A A A A A A A 290 D c T H C C C C C E A B C C F A A 291 A c T x B B A B B C A A A A B A A 292 L c c H A A A A B A A A A A A A A pdb-ss-model alr1.pdb alr1_xa.ss ribbons -n alr1
creates required files then displays the ribbon. The `Ribbon Style Panel' selects among `seq', `ss', etc., for per residue color codings.
Figure 5, a stereo drawing, has the `Eres' key selected to color the ribbon
based on residue error. Hot spots in the structure should be obvious. Dark
colors indicate problems here. A residue may be picked to display information.
The contour surface is created from a cofactor difference map in FRODO format. 
Figure 5. Residue error in preliminary Alr1 refinement.
Each user created file is eligible for display and editing as a separate graphics object. All files have a simple format. For example, each sphere file line has coordinates (xyz), radius, color code, and label. The file cal.sph from example 2 is shown below:
28.73 30.05 62.86 2.30 11 cal_471_X
Ribbons can write/read files to save/restore the current orientation, styles and scale factors, colors and lighting. Data from other programs may be reformatted to generate the lists of spheres, cylinders, or triangles for display. An example is the visualization of ribosomal models(11). Ribbons can output primitives suitable for input into several ray-tracing packages.
Ribbons saves raster images as Silicon Graphics (SGI) `*.rgb' files. Many utilities support this file format. Figure 6 is a final example compositing several (ribbons) images of the DNA/trp repressor complex (PDB entry 1tro.ent(12)). The figures were converted to PostScript for printing.
Figure 6. DNA/protein rendering styles.