The ribbonjr command produces a static secondary structure ribbon image of the displayed molecule(s). In addition to protein ribbons, ribbonjr can make ribbon images of nucleic acids, optionally using stylized representations of the nucleotide sugars and bases. By default, ribbonjr displays the ribbon drawing in a separate window. Clicking the left mouse button in the window will dismiss it.
Note that the command ribbon, in contrast, produces an interactively rotatable secondary structure ribbon.
The ribbonjr command is actually an alias that uses pdbrun to send data to the outside program ribbonjr. There are many command-line options, which are detailed fully in the ribbonjr manual page.
In order for the ribbonjr command to show the correct secondary structure of a protein, all backbone atoms (CA,C,N,O) in the residues of interest must be displayed, and the model must have been opened from a PDB file containing HELIX and SHEET records. If such records were not present, it is possible to compute the secondary structure information with the ksdssp command. Nucleic acid secondary structure is correctly rendered without such additional information.
By default, ribbonjr shows all displayed atoms, not just the ribbon. Sidechains may be shown in ball-and-stick mode or as spheres (see also VDW radii). The -a option will limit display to the ribbon only. To show a few key sidechains, but not all sidechains, restrict the display to backbone atoms only with
chain @ca,c,n,oand then display only the desired sidechains before running ribbonjr.
~disp :.water (sometimes necessary since water also contains atoms named O)