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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

membrane protein with lipophilicity coloring

Coloring by Molecular Lipophilicity Potential

Molecular lipophilicity potential (MLP) can be calculated for a protein and displayed with surface coloring using the command mlp or the Molecule Display icon . The image shows the photosynthetic reaction center from a purple sulfur bacterium, with MLP coloring on the molecular surface and membrane boundaries from OPM (Orientations of Proteins in Membranes entry 1eys). Blue and red balls represent the cytoplasmic and periplasmic sides of the bacterial inner membrane, respectively. Parts of the L, M, and H chains span the membrane, whereas the cytochrome subunit sits on the periplasmic side, at the top. The surface coloring ranges from dark goldenrod for the most hydrophobic potentials, through white, to dark cyan for the most hydrophilic. Ligands including lipid, detergent, heme, and various other cofactors are shown as purple surfaces.

For image setup after the structure from OPM has been opened, see the command file mlp.cxc.

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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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