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Recent Citations

K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac. Dong YY, Pike AC et al. Science. 2015 Mar 13;347(6227):1256-1259.

Structure of the F-actin-tropomyosin complex. von der Ecken J, Müller M et al. Nature. 2015 Mar 5;519(7541):114-7.

AAV-expressed eCD4-Ig provides durable protection from multiple SHIV challenges. Gardner MR, Kattenhorn LM et al. Nature. 2015 Mar 5;519(7541):87-91.

Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins. Soltan Ghoraie L, Burkowski F, Zhu M. Proteins. 2015 Mar;83(3):497-516.

Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures. Kosinski J, von Appen A et al. J Struct Biol. 2015 Mar;189(3):177-83.

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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

structure-based sequence alignment superimposed structures

Structure-Based Sequence Alignment

Given two or more superimposed structures, Match→Align creates a corresponding sequence alignment. The user specifies a distance cutoff for residues allowed to be in the same column of the output alignment. In proteins, the distances are measured between α-carbons. The method is independent of residue types and how the structures were superimposed.
The figure shows a superposition from MatchMaker of five proteins from the SCOP WD40 superfamily and a corresponding sequence alignment from Match→Align, automatically shown in Multalign Viewer. In the sequence alignment, light green and yellow boxes indicate strands and helices, while the headers RMSD and Conservation show spatial and sequence conservation, respectively.

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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...)