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

Conformational dynamics of a multienzyme complex in anaerobic carbon fixation. Yin MD, Lemaire ON et al. Science. 2025 Jan 31;387(6733):498-504.

Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription. Markert JW, Soffers JH, Farnung L. Science. 2025 Jan 31;387(6733):528-533.

Novel lineage of anelloviruses with large genomes identified in dolphins. De Koch MD, Krupovic M et al. J Virol. 2025 Jan 31;99(1):e0137024.

Native DGC structure rationalizes muscular dystrophy-causing mutations. Liu S, Su T et al. Nature. 2025 Jan 30;637(8048):1261–1271.

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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

cyclodextrin pore

Cyclodextrin Pore

The outer-membrane protein CymA admits bulky molecules into the periplasmic space of Klebsiella oxytoca. Here, CymA (PDB 4d5d chain A) is depicted in a style reminiscent of a diagnostic X-ray, with transparent molecular surface and β-strand “ribs” in white. The protein has ingested α-cyclodextrin (top) and β-cyclodextrin (bottom), bound at the entry site and near the exit, respectively. Cyclodextrin carbon atoms are shown in blue-gray and oxygen atoms in brick red. For image setup, see the command file xray.cxc.

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