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Recent Citations

The structure of the human mitochondrial ribosome. Amunts A, Brown A et al. Science. 2015 Apr 3;348(6230):95-8.

A large-scale genetic analysis reveals a strong contribution of the HLA class II region to giant cell arteritis susceptibility. Carmona FD, Mackie SL et al. Am J Hum Genet. 2015 Apr 2;96(4):565-80.

Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase. Fenwick MK, Mehta AP et al. Nat Commun. 2015 Mar 27;6:6480.

Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components. Gerling T, Wagenbauer KF et al. Science. 2015 Mar 27;347(6229):1446-1452.

Crystal structure of the eukaryotic origin recognition complex. Bleichert F, Botchan MR, Berger JM. Nature. 2015 Mar 19;519(7543):321-6.

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Chimera Search

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News

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.

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.

(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

dopamine receptor with axes and planes

Axes and Planes

Axes, planes, and centroids can be calculated from sets of atoms using the Axes/Planes/Centroids tool or the command define. Axes can be shown as cylinders, planes as disks, and centroids as spheres, and any of these can be used in distance and angle measurements.

For example, the figure shows the dopamine D3 receptor and bound inhibitor (PDB entry 3pbl) as modeled into the membrane in the OPM database. The planes of the inner and outer membrane boundaries are shown as transparent blue and red disks, respectively. The protein ribbon is rainbow-colored from blue at the N-terminus to red at the C-terminus, and the axis of each helix is shown as a cylinder of matching color. The axis of the red helix forms an angle of 15.1° with the membrane and comes within 3.5 Å of the inner boundary. The yellow and orange helices are nearly antiparallel (crossing angle 5.9°). The average (minimum, maximum) distance of inhibitor atoms from the outer boundary is 7.9 (5.1, 11.7) Å.

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Gallery Sample

G Protein Interface Surface

Heterotrimeric G protein (Protein Data Bank entry 1gg2) with the alpha subunit shown in green, the beta subunit in light blue, and the gamma subunit in brown. The Intersurf tool was used to show the interface between the alpha and beta subunits. The interface surface is colored to show the distance between atoms across the interface (red for closer together, blue for farther apart). (More samples...)