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Computationally restoring the potency of a clinical antibody against Omicron. Desautels TA, Arrildt KT et al. Nature. 2024 May 23;629(8013):878–885.

Mechanism of single-stranded DNA annealing by RAD52-RPA complex. Liang CC, Greenhough LA et al. Nature. 2024 May 16;629(8012):697–703.

Structural and functional characterization of the interaction between the influenza A virus RNA polymerase and the CTD of host RNA polymerase II. Keown J, Baazaoui A et al. J Virol. 2024 May 14;98(5):e0013824.

Structures and activation mechanism of the Gabija anti-phage system. Li J, Cheng R et al. Nature. 2024 May 9;629(8011):467–473.

Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. Ketaren NE, Mast FD et al. eLife. 2024 May 7;12:RP89423.

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News

January 22, 2024

ChimeraX 1.7.1 is available, with fixes for a few miscellaneous bugs that were identified after the 1.7 release.

December 19, 2023

The ChimeraX 1.7 production release is available! See the change log for what's new. Future Mac releases will require macOS 11 or higher.

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.

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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

mitochondrial import receptor subunit TOMM40

AlphaFold Fetch

AlphaFold is an artificial intelligence method for predicting protein structures. With the AlphaFold tool or command, ChimeraX can search for and load predicted structures from the freely available AlphaFold Database, automatically coloring them by confidence value:

  • 100
    to 90
    – high accuracy
  • 90
    to 70
    – backbone accuracy
  • 70
    to 50
    – low confidence, caution
  • 50
    to 0
    – should not be interpreted, may be disordered

The figure shows the predicted structure of UniProt entry TOM40_HUMAN, a channel protein needed to import other proteins into mitochondria. See the command file tom40.cxc for fetching data and other setup (background color, etc.).

Opening a sequence from UniProt also opens a dialog in which its annotations or “features” can be clicked to highlight those regions in both the sequence and the associated 3D structure. The low-confidence part of this structure (orange and red) maps to compositionally biased and likely disordered regions near the N-terminus of the sequence.

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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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