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Recent Citations

Structures of the M1 and M2 muscarinic acetylcholine receptor/G-protein complexes. Maeda S, Qu Q et al. Science. 2019 May 10;364(6440):552-557.

Visualization of clustered protocadherin neuronal self-recognition complexes. Brasch J, Goodman KM et al. Nature. 2019 May 9;569(7755):280-283.

Three-dimensional architecture of epithelial primary cilia. Sun S, Fisher RL et al. Proc Natl Acad Sci USA. 2019 May 7;116(19):9370-9379.

A compact synthetic pathway rewires cancer signaling to therapeutic effector release. Chung HK, Zou X et al. Science. 2019 May 3;364(6439). pii: eaat6982.

Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes. Abbas A, He X et al. Nat Commun. 2019 May 3;10(1):2049.

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News

November 17, 2018

Chimera production release 1.13.1 is now available; see the release notes for what's new. The Mac version requires OS 10.10 or later.

October 22, 2018

Mac users: the 1.13.1 release candidate and recent daily builds contain a fix for Mojave (OS 10.14). These versions require OS 10.10 or later.

September 21, 2018

Mac users are advised to hold off upgrading to Mojave until we find a fix for Chimera buttons not being shown until the windows containing them are resized.

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Upcoming Events

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), supported in part by the National Institutes of Health (P41-GM103311).

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the RBVI, following UCSF Chimera.

Feature Highlight

1ovh pocket list 1ovh pockets

CASTp Pocket Data

Structures and their pocket measurements can be fetched directly from the Computed Atlas of Surface Topography of proteins (CASTp) database or read from local files previously returned by the CASTp server. In Chimera, the pockets are shown in a pocket list. Choosing rows in the list performs actions such as zooming in on pockets and selecting the surrounding atoms.

The figure shows the four largest pockets by volume identified by CASTp for PDB entry 1ovh (a cavity mutant of T4 lysozyme), shown in yellow, orange, pink, and magenta in order of decreasing volume. The largest is lysozyme's active site, with two openings. The second largest is the engineered cavity. Mutated positions are shown in red. Green balls are Cl ions.

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Gallery Sample

Peroxiredoxin Wreath

Peroxiredoxins are enzymes that help cells cope with stressors such as high levels of reactive oxygen species. The image shows a decameric peroxiredoxin from human red blood cells (Protein Data Bank entry 1qmv), styled as a holiday wreath.

See also the RBVI holiday card gallery.

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