home overview research resources outreach & training outreach & training visitors center visitors center search search

Quick Links

Recent Citations

A molecular ruler determines the repeat length in eukaryotic cilia and flagella. Oda T, Yanagisawa H et al. Science. 2014 Nov 14;346(6211):857-60.

Drug sensing by the ribosome induces translational arrest via active site perturbation. Arenz S, Meydan S et al. Mol Cell. 2014 Nov 6;56(3):446-52.

Allosteric signalling in the outer membrane translocation domain of PapC usher. Farabella I, Pham T et al. eLife. 2014 Oct 28;3.

Molecular basis for the ribosome functioning as an L-tryptophan sensor. Bischoff L, Berninghausen O, Beckmann R. Cell Rep. 2014 Oct 23;9(2):469-75.

Structural mechanism of glutamate receptor activation and desensitization. Meyerson JR, Kumar J et al. Nature. 2014 Oct 16;514(7522):328-34.

(Previously featured citations...)

Chimera Search

Google™ Search

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).

(Previous news...)

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.

(More features...)

Gallery Sample

Annotated Green Fluorescent Protein

BILD format was used in Chimera to annotate the barrel structure of green fluorescent protein with its centroid, major axis (red arrow), and an enclosing cylinder (shown with green hoops). The BILD file green.bild was generated with the python program green.py using the coordinates in green.pdb. Gallery entry courtesy of Mike Ess, Yeast Resource Center, University of Washington. (More samples...)