e29 Nucleic Acids Research, 2006, Vol. 34, No. 4 available within the Chimera package and available from the Chimera web site (http://www.cgl.ucsf.edu/chimera/). The new features available in the Nucleotides extension are discussed below, and examples of the features can be seen in Figures 2–7 and in the image gallery on the Chimera web site. All features are easily accessible via a menu interface within Chimera, as shown in Figure 1. Representations of sugars The furanose ring found in nucleic acids generally takes either the envelope form, with four atoms in a plane, or the twist form, with three atoms in a plane and two adjacent atoms on either side of that plane (18). We have created a new repres- entation to emphasize the plane and twist forms of the ring. This representation is unique to the Chimera Nucleotides extension. In order to elucidate sugar pucker, we ﬁll the furanose ring by drawing either two or four planes. For the envelope form, a single atom is out of the plane, so we draw two planes: one deﬁned by the four atoms in-plane, and a triangle that extends to the outlying atom. For the twist form, we emphasize the location of the twist by drawing one plane deﬁned by the three atoms in-plane together with a fourth point located towards the twist of the ring and combine this with three triangles con- necting the other atoms (Figure 2). The decision of when to consider atoms coplanar and thus which form to use when drawing a sugar is driven by geometric considerations only; in the future we plan to add an option so that the user can adjust PAGE 2 OF 5 the threshold for controlling this behavior. (Source code for the representation of sugars is available in the Supplementary Data.) Another abstraction of the sugar is as a tube that connects the base to the backbone (atoms or ribbon). The tube is drawn from the C40 atom of the sugar to the N1 atom of the base for pyrimidines or N9 for purines. If the user chooses to display the glycosidic bond, then the tube terminates at the sugar C10. Thus, the simpliﬁed connection of base to backbone can either by shown as a single cylinder (as in the G–C pairs in Figure 4) or as two cylinders broken at the C10 (as in Figures 3 and 5). Backbone ribbon In order to more accurately represent the backbone of the nucleic acid, we modiﬁed the ribbon representation that is used for proteins. For proteins, we draw a ribbon with the backbone oxygen as the orientation atom, and the backbone alpha carbon as the guide atom, with the resulting ribbon perpendicular to the side chain. For nucleic acids, we choose C10 as the orientation atom and C50 as the guide atom, both located in the sugar. Similar to the method ﬁrst described by Carson and Bugg (19), our ribbon representations are based on B-splines (20) with the coordinates of the guide atoms used as spline control points and the orientation atom used to deter- mine the plane of the ribbon. But with the default approach used for proteins, the resulting ribbon was parallel to the base rather than perpendicular. We created a new option for ribbon representations for nucleic acids such that the ribbon axis is rotated by 90 , and the resulting backbone ribbon is perpen- dicular to the bases (Figure 3). The original representation of the ribbon remains available as the ‘classic ribbon’ option in the Nucleotides menu. Additional options to the ribbon, such as changing the cross-section of the ribbon, are available as a standard option within Chimera’s Ribbon Style Editor menu Figure 1. The Nucleotides menu for the nucleic acid visualization tool, showing the many options for the display of the backbone, sugars and bases. Chimera has separate menus for controlling the parameters used for coloring and for drawing ribbons. See http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ nucleotides/nucleotides.html for a detailed description. Figure 2. Sugar pucker, in the envelope form (red) and twist form (yellow). The envelope form is highlighted using two planes, while the twist form is accented by the drawing of four planes, achieved by the introduction of a non-atom vertex.