e29 Nucleic Acids Research, 2006, Vol. 34, No. 4 PAGE 4 OF 5 Figure 5. Netropsin bound to double-stranded DNA (28) (PDB identifier 6bna). Each strand of the DNA is colored with the ‘rainbow’ option, with the base colors changing over a range from blue to red from the 50 to the 30 end, respectively. The DNA is shown with the backbone represented as a smooth ribbon, the sugars drawn as elliptical tubes and the bases as ellipsoids. Netropsin is colored by element and shown in the ball-and-stick representation, with a transparent pink molecular surface. Figure 6. The Thermus thermophilus 30S ribosomal subunit (7) (PDB identifier 1j5e). Drawn with the Nucleotides extension and Chimera’s MultiScale exten- sion (26), the single-stranded RNA chain is colored with the rainbow option, and the proteins are shown as low-resolution surfaces. From this perspective, the helices appear to be formed from local interactions within the RNA, e.g. red bases pairing with other red bases and green bases pairing with other green bases. Tertiary interactions between the differently colored helices are high- lighted as the different colored helices are brought together. Distinct from the other figures, the ribbon representation of the 16S ribosomal RNA has a rounded cross-section, and thus its smooth edges make the orientation of the ribbon less visible. of bases as slabs and ellipsoids, a modiﬁed ribbon backbone and a new representation of sugar geometry. While other approaches provide beautiful representations, e.g. the ribbon representations of nucleic acids available in the Ribbons (24) and DRAWNA (25) programs, and are integrated into existing, interactive software packages, such as the nuccyl extension (http://www.biosci.ki.se/groups/ljo/software/nuccyl.html) to PyMol (http://pymol.sourceforge.net/), our tools are unique in their representations of sugar pucker, base sidedness and Figure 7. The Escherichia coli L25 ribosomal protein with 5S ribosomal RNA fragment (29) (PDB identifier 1dfu). Atomic interactions are highlighted be- tween the RNA and the protein by filling the base and sugar rings and leaving the nucleic acid backbone fully represented. The protein is drawn in the stick representation, and the bound metal ions are in yellow. Hydrogen bonds be- tween the RNA and protein were calculated by Chimera and are drawn in yellow. ease of changing between alternative conventions. As part of UCSF Chimera, the Nucleotides extension is integrated with a mature, well-supported software suite and can easily be used in conjunction with Chimera’s chemical knowledge (e.g. hydrogen bonding and atom typing) and multi-scale models (26) for large molecules (i.e. ribosomes, viruses, nucleosome core). SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. ACKNOWLEDGEMENTS This work has been supported by NIH grants P41 RR001081 (to TE Ferrin) and R01 GM066199 (to SR Holbrook). The authors thank Nikolai B. Ulyanov for numerous helpful discussions, and Steven E. Brenner and Stephen R. Holbrook for their encouragement. Funding to pay the Open Access publication charges for this article was provided by NIH grant P41 RR001081. Conflict of interest statement. None declared. REFERENCES 1. Batey,R.T., Gilbert,S.D. and Montange,R.K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411–415. 2. Serganov,A., Yuan,Y.R., Pikovskaya,O., Polonskaia,A., Malinina,L., Phan,A.T., Hobartner,C., Micura,R., Breaker,R.R. and Patel,D.J. (2004)