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Cryo-EM structure of the human cardiac myosin filament. Dutta D, Nguyen V et al. Nature. 2023 Nov 23;623(7988):853–862.

Structure of the native myosin filament in the relaxed cardiac sarcomere. Tamborrini D, Wang Z et al. Nature. 2023 Nov 23;623(7988):863–871.

Autoregulatory control of mitochondrial glutathione homeostasis. Liu Y, Liu S et al. Science. 2023 Nov 17;382(6672):eadf4154.

Rapid bacteria-phage coevolution drives the emergence of multiscale networks. Borin JM, Lee JJ et al. Science. 2023 Nov 10;382(6671):674-678.

OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis. Luo Z, Ni F et al. Nat Methods. 2023 Nov;20(11):1729-1738.

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November 6, 2023

The ChimeraX 1.7 release candidate is available – please try it and report any issues. See the change log for what's new.

October 30-31, 2023

Planned downtime: The ChimeraX website, associated web services, and Toolshed will be unavailable Oct 30 8am PDT – Oct 31 11:59pm PDT.

October 4, 2023

New paper online: UCSF ChimeraX: Tools for structure building and analysis. Meng EC, Goddard TD, et al. Protein Sci. 2023, in press.

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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

Morphing Movie

Morphing between atomic structures can be calculated wih the morph command and played back in an animation. This movie shows morphing between two conformations of the FGFR1 kinase domain:

  • inactive structure (PDB 3c4f, chain A)
  • activated structure (PDB 3gqi, chain A) with phosphorylated tyrosines and bound ATP analog
The tyrosine side chains and ATP analog are color-coded by element: light blue carbon, red oxygen, blue nitrogen, and orange phosphorus.

Morphing and other setup was done with the command file kmorph-prep.cxc, followed by interactively positioning the structure and saving the view with the command view name p1 (generally a session would also be saved at this point), then running kmorph-play.cxc to add 2D labels and record the movie.

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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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