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Structural basis of odorant recognition by a human odorant receptor. Billesbølle CB, de March CA et al. Nature. 2023 Mar 23;615(7953):742–749.

Structures of BIRC6-client complexes provide a mechanism of Smac-mediated release of caspases. Hunkeler M, Jin CY, Fischer ES. Science. 2023 Mar 17;379(6637):1105-1111.

Blebs promote cell survival by assembling oncogenic signalling hubs. Weems AD, Welf ES et al. Nature. 2023 Mar 16;615(7952):517-525.

Coordination of bacterial cell wall and outer membrane biosynthesis. Hummels KR, Berry SP et al. Nature. 2023 Mar 9;615(7951):300–304.

Architecture of chloroplast TOC-TIC translocon supercomplex. Liu H, Li A et al. Nature. 2023 Mar 9;615(7951):349–357.

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News

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.

December 20, 2022

Brought to you by the Brown Lab at Virginia Tech: ChimeraX Tutorial: Making a Holiday Tree!

November 23, 2022

The ChimeraX 1.5 production release is available! 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

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

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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