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Featured Citations

Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome. Yatskevich S, Muir KW et al. Science. 2022 May 20;376(6595):844-852.

The tethered peptide activation mechanism of adhesion GPCRs. Barros-Álvarez X, Nwokonko RM et al. Nature. 2022 Apr 28;604(7907):757–762.

Structural basis for the tethered peptide activation of adhesion GPCRs. Ping YQ, Xiao P et al. Nature. 2022 Apr 28;604(7907):763–770.

Structure of ATP synthase under strain during catalysis. Guo H, Rubinstein JL. Nat Commun. 2022 Apr 25;13(1):2232.

Mechanism of RNA polymerase I selection by transcription factor UAF. Baudin F, Murciano B et al. Sci Adv. 2022 Apr 22;8(16):eabn5725.

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News

December 20, 2021

The RBVI wishes you a safe and happy holiday season! See our 2021 card and the gallery of previous cards back to 1985.

December 8, 2021

The ChimeraX 1.3 production release is available. See the change log for what's new.

October 22, 2021

The ChimeraX 1.3 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 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases.

Feature Highlight

AMPA receptor with tube helices

Curved Helix Cylinders

Protein α-helices can be shown as curved-cylinder “tubes“ with the cartoon style command. Helix tube mode is an alternative to the standard spiraling ribbons, and both modes are fully integrated with coil and β-strand cartoons. The structure at left is an AMPA-subtype glutamate receptor bound to the antiepileptic drug perampanel (PDB 5l1f). The receptor is tetrameric, and each chain is rainbow color-coded from blue at the N-terminus to red at the C-terminus. Four molecules of perampanel (pink) are bound near the bottom, between the transmembrane domain and the rest of the receptor. For image setup other than orientation, see the command file ampar.cxc.

See also: Presets menu

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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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