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Transcriptome-wide splicing network reveals specialized regulatory functions of the core spliceosome. Rogalska ME, Mancini E et al. Science. 2024 Nov 1;386(6721):551-560.

LYCHOS is a human hybrid of a plant-like PIN transporter and a GPCR. Bayly-Jones C, Lupton CJ et al. Nature. 2024 Oct 31;634(8036):1238–1244.

Glucose-sensitive insulin with attenuation of hypoglycaemia. Hoeg-Jensen T, Kruse T et al. Nature. 2024 Oct 24;634(8035):944-951.

A brain-to-gut signal controls intestinal fat absorption. Lyu Q, Xue W et al. Nature. 2024 Oct 24;634(8035):936-943.

Heteromeric amyloid filaments of ANXA11 and TDP-43 in FTLD-TDP type C. Arseni D, Nonaka T et al. Nature. 2024 Oct 17;634(8034):662–668.

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News

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.

June 17-18, 2024

Planned downtime: The ChimeraX website, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable June 17-18 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

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

CaM-CaMKI peptide

Calmodulin and Target Peptide

Calmodulin (CaM) acts as a calcium sensor. When its four Ca++ sites are fully occupied, it binds and modulates the activity of various downstream proteins, including CaM-dependent protein kinase I (CaMKI). Here, a complex between CaM and its target peptide from CaMKI (PDB 1mxe) is shown with cartoons, a transparent molecular surface, silhouette outlines, and light soft ambient occlusion. (If you prefer a less smudgy/rustic appearance, try using light gentle instead.) For image setup other than positioning, see the command file cam.cxc.

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