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Recent Citations

Escape from bacterial iron piracy through rapid evolution of transferrin. Barber MF, Elde NC. Science. 2014 Dec 12;346(6215):1362-6.

Ultrastable gold substrates for electron cryomicroscopy. Russo CJ, Passmore LA. Science. 2014 Dec 12;346(6215):1377-80.

Cryo-electron tomography reveals ciliary defects underlying human RSPH1 primary ciliary dyskinesia. Lin J, Yin W et al. Nat Commun. 2014 Dec 4;5:5727.

Structures of protective antibodies reveal sites of vulnerability on Ebola virus. Murin CD, Fusco ML et al. Proc Natl Acad Sci USA. 2014 Dec 2;111(48):17182-7.

Structure of a designed protein cage that self-assembles into a highly porous cube. Lai YT, Reading E et al. Nat Chem. 2014 Dec;6(12):1065-71.

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News

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.

October 23, 2014

A production release candidate (v1.10) is available; please try it and report any problems. 64-bit builds are now 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.

August 15, 2014

We are delighted to announce the publication of a new book, Computational and Visualization Techniques for Structural Bioinformatics Using Chimera, written by Forbes J. Burkowski (University of Waterloo).

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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

Loop Interactions

The image shows interactions of the delta-1 loop with the rest of hepatitis C virus RNA-dependent RNA polymerase (Protein Data Bank entry 1quv). Loop residues in contact with the rest of the structure (van der Waals overlap ≥ 0.01 Å) are displayed as sticks; interacting surface atoms are shown as red patches. (More samples...)