Many of the ideas on illustrating molecular properties of interest to the crystallographer were presented earlier (Carson and Bugg, 1988). The agreement of electron density fit was previously determined by an unpublished method. The real space R-factor (Jones et al., 1991) appears to be a superior method. The assignment of sidechain sensibilities by O does not appear to be as good as this implementation. The color-coding by energetics was originally done with the CEDAR and SPRUCE programs (Carson and Hermans, 1984). X-PLOR is now used for such computations, due to the flexibility and power of its shell language. For example, a separate program was originally used to determine rms temperature factors for each residue, mainchain, and sidechain. This has been replaced by composing a simple X-PLOR script. The program package provides sample scripts for displaying a variety of analyses from X-PLOR and for displaying the real space fit from O.
The ribbon drawing presents a global view of the molecule: color cues and irregularities in the ribbon are immediately picked up by the human visual system. This is useful to the crystallographer in assessing the validity of the coordinates in question. Ribbon drawings have been observed to become `smoother' during the course of structural refinement of proteins. Work on the quantification of this point is in progess.
Ribbon drawings make striking illustrations. Keats' line that truth is beauty may be applicable here. I would like to encourage those with more mathematical sophistication than the author to investigate the space curve underlying the ribbon construction --- perhaps it holds a key to the protein folding problem.
I would like to thank Dr. Charles E. Bugg for his encouragement and support. This work was made possible by NASA grant NAGW813. A grant from the Alabama Research Council allowed the purchase of the IRIS workstation.
This program is licensed at nominal charge to academics (our laboratory's NASA grant urges the commercialization of our work). A user's manual, C source code, UNIX Makefiles, sample data, sample images, and E-mail support are provided.