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Recent Citations

Biogenesis and structure of a type VI secretion membrane core complex. Durand E, Nguyen VS et al. Nature. 2015 Jul 30;523(7562):555-60.

Structural and biochemical characterization of AidC, a quorum-quenching lactonase with atypical selectivity. Mascarenhas R, Thomas PW et al. Biochemistry. 2015 Jul 21;54(28):4342-53.

A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly. Dodonova SO, Diestelkoetter-Bachert P et al. Science. 2015 Jul 10;349(6244):195-198.

Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers. Fibriansah G, Ibarra KD et al. Science. 2015 Jul 3;349(6243):88-91.

The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Nguyen TH, Galej WP et al. Nature. 2015 Jul 2;523(7558):47-52.

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News

July 23, 2015

Chimera production release 1.10.2 is now available. Fixes include code signing for Mac OS X installation. The 1.10 series will be the last to support OS X 10.6 and 10.7. See the release notes for details.

January 9, 2015

Chimera production release 1.10.1 is now available. 64-bit builds are recommended for all capable platforms, and the 1.10 series will be the last to support OS X 10.6 and 10.7. See the release notes for details.

November 5, 2014

Chimera production release 1.10 is now available. 64-bit builds are recommended for all capable platforms, and v1.10 will be the last to support OS X 10.6 and 10.7. See the release notes for what's new.

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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, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics, funded by the National Institutes of Health (NIGMS P41-GM103311).

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

Cavity and Tunnel Detection

Side-by-side views of a potassium channel structure (Protein Data Bank entry 1bl8) showing different approaches to cavity detection. On the left are molecular surface patches corresponding to the structure's two largest pockets by MS volume in the Computed Atlas of Surface Topography of proteins (CASTp) database. On the right is a tunnel in blue identified by the MolAxis server. Simple editing converted MolAxis output into a BILD file for display in Chimera. (More samples...)