PAGE 3 OF 5 Nucleic Acids Research, 2006, Vol. 34, No. 4 e29 Figure 3. Backbone ribbon representations of B-form DNA (PDB identifier 1bna) (27). In the image on the left, the ribbon is drawn with the C10 atom, located in the sugar, as the orientation atom and the plane of the ribbon along the sugar. The image on the right shows the new nucleic acid ribbon representation, with the ribbon axis rotated by 90 . and the color of the backbone ribbon is customizable by the user. Bases Base stacking is a key structural feature and is important for the stabilization of nucleic acids (18). Visual emphasis of this feature was one of the motivating factors for building the Nucleotides extension to Chimera. Four representations of bases are available: ﬁlled, box slab (or box), elliptical tube slab and ellipsoid slab. Examples are shown in Figure 4. In order to display the orientation of the base, each base is drawn with a rounded protuberance (a dot) at the center of each ring on the positive face [as described in Olson et al. (21)] of the base. The positive face of the base is deﬁned by a coordinate frame such that, in an idealized right-handed A-form or B-form helix, the X-axis points toward the major groove, the Y-axis is parallel to a C10–C10 vector within paired bases, and the Z-axis points along the 50–30 direction. In the case of A- or B-form helices, dots appear on the 50 side of the bases. The ﬁlled base option simply ﬁlls the rings of the pyrimi- dines and purines. By selecting this option, the user preserves the purine versus pyrimidine identity of the base, but also emphasizes the position of the base by simply making the rings much more visible. The slab options are designed to emphasize base pairing and stacking. With bases displayed in the box formation the ‘spiral stair case’ quality of a helix is much more prominent than with the ﬁlled or atom/bond representation (as shown in Figure 4). Several options for the position and size of the slab with respect to the base are available, as well as a custom setting, and these settings are easily obtained by the user through a simple interface. The default setting for the slab option draws the slab as a box, with the purine box anchored at the base N9 and the pyrimidine box anchored at the base N1. The default slab covers most of the base, and extends slightly beyond the base rings to Figure 4. Base representations, including, from top to bottom, filled rings, boxes, ellipsoids and elliptical tubes. emphasize base pairing. The user can also adjust the thickness of the box. Additional representations of bases are displayed in Figure 4. These include the platter-like ellipsoid and the elliptical tube, which is elliptical in cross-section, along the axis of the p-orbitals of the base, but with the rings abstrac- ted as squares or rectangles, much like the slab representation. In addition to multiple representation of the bases, the Nucleotides extension also offers a quick way to color bases by the NDB convention (22) by selecting the ‘NDB Colors’ button, with yellow for C, red for A, green for G, cyan for U, and blue for T. Bases may also be colored using the Rainbow tool, varying in color from blue at the 50 end to red at the 30 end of a chain, and may be colored in numerous other ways, all standard within Chimera, includ- ing by atom, by residue and by chain. The backbone ribbon color can differ from the color of the base. RESULTS Several examples of our new representations of nucleic acids can be seen in Figures 5–7, for both DNA and RNA molecules and their complexes. (Refer to the ﬁgure captions for explan- atory details.) The representations described here are easily created from menu- and command-line options within Chi- mera and the representations are drawn on-demand, quickly and interactively, and publication-quality ﬁgures can be generated from the interactive sessions. DISCUSSION This report describes a new set of tools for nucleic acid visu- alization that are packaged as extensions to the UCSF Chimera molecular visualization suite. The original goals of the exten- sions were to emphasize base stacking, rearrange the ribbon and attempt to create and extend the kinds of representations often seen in textbooks (23). The new representations for nucleic acids include ﬁlled bases, alternate representations