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Featured Citations

Bat genomes illuminate adaptations to viral tolerance and disease resistance. Morales AE, Dong Y et al. Nature. 2025 Feb 13;637(8050):449–458.

C-terminal amides mark proteins for degradation via SCF-FBXO31. Muhar MF, Farnung J et al. Nature. 2025 Feb 13;637(8050):519–527.

Resolving native GABAA receptor structures from the human brain. Zhou J, Noviello CM et al. Nature. 2025 Feb 13;637(8050):562–568.

Four-component protein nanocages designed by programmed symmetry breaking. Lee S, Kibler RD et al. Nature. 2025 Feb 13;637(8050):546–552.

Crosslinking intermodular condensation in non-ribosomal peptide biosynthesis. Heberlig GW, La Clair JJ, Burkart MD. Nature. 2025 Feb 6;637(8049):261–269.

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News

December 25, 2024

The RBVI wishes you a safe and happy holiday season! See our 2024 card and the gallery of previous cards back to 1985.

December 12, 2024

The ChimeraX 1.9 production release is available! See the change log for what's new.

October 14, 2024

Planned downtime: The ChimeraX website, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable starting Monday, Oct 14 10 AM PDT, continuing throughout the week and potentially the weekend (Oct 14-20).

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UCSF ChimeraX

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use. Commercial users, please see ChimeraX commercial licensing.

ChimeraX is developed with support from National Institutes of Health R01-GM129325, Chan Zuckerberg Initiative grant EOSS4-0000000439, and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases.

Feature Highlight

1pho trimer with bfactor coloring/worms

Worms

Worms are specialized cartoons in which “fatness” reflects the values of an attribute such as bfactor or seq_conservation. In the example image, the average atomic B-factor per amino acid residue is shown with both coloring and worms. The structure is a trimer of E. coli porin (PDB 1pho). For image setup, see the command file worms.cxc.

Worms are available in ChimeraX v1.8 daily builds 3/12/24 and newer. Worms and coloring by attribute can be done with the Render by Attribute tool or commands cartoon byattribute (aka worm) and color byattribute.

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Example Image

transducin switch regions

G-Protein Switch Regions

The GDP- and GTP-bound conformations of the transducin α-subunit (1tag and 1tnd, respectively) differ primarily in three regions, termed switch 1, switch 2, and switch 3. The structures have been superimposed with matchmaker and shown as cartoons, with “empty” outlines where the structures are almost the same (for simplicity, only one conformation's outlines are shown). The GTP analog GTPγS is displayed as spheres color-coded by heteroatom. For 2D labels and image setup other than structure orientation, see the command file switch.cxc.

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