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Featured Citations

Tracking transcription-translation coupling in real time. Qureshi NS, Duss O. Nature. 2025 Jan 9;637(8045):487–495.

Autoinhibition of dimeric NINJ1 prevents plasma membrane rupture. Pourmal S, Truong ME et al. Nature. 2025 Jan 9;637(8045):446–452.

Chemical bond overlap descriptors from multiconfiguration wavefunctions. Santos-Jr CV, Kraka E, Moura RT Jr. J Comput Chem. 2025 Jan 5;46(1):e27534.

Stereochemistry in the disorder-order continuum of protein interactions. Newcombe EA, Due AD et al. Nature. 2024 Dec 19;636(8043):762–768.

Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine. Wang C, Kassem S et al. Nat Commun. 2024 Dec 17;15(1):10689.

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News

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).

August 1, 2024

Planned downtime: The ChimeraX website, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable August 1, 3-6 pm PDT.

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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

man and molecule

Virtual Reality

ChimeraX virtual reality works with HTC Vive, Oculus Rift, and Samsung Odyssey systems (those supported by SteamVR). Any structures, maps, etc. that can be displayed in ChimeraX can be viewed in the headset and manipulated with the hand controllers. Icon toolbars visible in the headset allow changing the scene display or hand-controller button assignments with a single click. Besides rotation, translation, and zooming, useful functions include labeling, distance measurement, bond rotation, placing markers into a map, and changing map contour levels. Virtual-reality (VR) mode can be turned on and off with the vr command, and the meeting command allows multiple users to share a single session in VR.

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Example Image

HIV-1 protease B-factor coloring

B-factor Coloring

Atomic B-factor values are read from PDB and mmCIF input files and assigned as attributes that can be shown with coloring and used in atom specification. This example shows B-factor variation within a structure of the HIV-1 protease bound to an inhibitor (PDB 4hvp). For complete image setup, including positioning, color key, and label, see the command file bfactor.cxc.

Additional color key examples can be found in tutorials: Coloring by Electrostatic Potential, Coloring by Sequence Conservation

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