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Featured Citations

DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in Caenorhabditis elegans. Xia Y, Sonneville R et al. Science. 2023 Sep 22;381(6664):eadi4932.

Central role of Tim17 in mitochondrial presequence protein translocation. Fielden LF, Busch JD et al. Nature. 2023 Sep 21;621(7979):627–634.

Conserved class B GPCR activation by a biased intracellular agonist. Zhao LH, He Q et al. Nature. 2023 Sep 21;621(7979):635–641.

Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation. Juyoux P, Galdadas I et al. Science. 2023 Sep 15;381(6663):1217-1225.

Oligomerization-mediated activation of a short prokaryotic Argonaute. Shen Z, Yang XY et al. Nature. 2023 Sep 7;621(7977):154–161.

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News

May 9, 2023

The ChimeraX 1.6.1 production release is available! See the change log for what's new.

April 29, 2023

The ChimeraX 1.6 release candidate is available – please try it and report any issues. See the change log for what's new.

December 21, 2022

The RBVI wishes you a safe and happy holiday season! See our 2022 card and the gallery of previous cards back to 1985.

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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

2ptt interchain H-bonds screenshot

Interactive H-Bond Histogram

Hydrogen bonds (H-bonds) can be identified with the H-Bonds tool, hbonds command, or the Molecule Display icon and plotted as an interactive histogram with the command crosslinks histogram.

The ChimeraX graphics window shows the complex between a natural killer cell receptor 2B4 and its ligand CD48 (PDB 2ptt). The receptor protein is blue, the ligand protein pink, and H-bonds between them dashed yellow, with H-bonding residues labeled. Although not done here, the H-bonds could also be labeled by distance.

The histogram of H-bond distances on the top right is interactive: when the cursor is placed over a bar in the histogram, the corresponding H-bonds are temporarily enlarged in the 3D view and the others hidden. For image setup other than orientation, see the command file hb3.cxc.

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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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