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Recent Citations

Spatial localization of the Ebola virus glycoprotein mucin-like domain determined by cryo-electron tomography. Tran EE, Simmons JA et al. J Virol. 2014 Sep 15;88(18):10958-62.

A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. McHugh CA, Fontana J et al. EMBO J. 2014 Sep 1;33(17):1896-911.

A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Geary C, Rothemund PW, Andersen ES. Science. 2014 Aug 15;345(6198):799-804.

Activating mutations in RRAS underlie a phenotype within the RASopathy spectrum and contribute to leukaemogenesis. Flex E, Jaiswal M et al. Hum Mol Genet. 2014 Aug 15;23(16):4315-27.

Predicted structure and domain organization of rotavirus capping enzyme and innate immune antagonist VP3. Ogden KM, Snyder MJ et al. J Virol. 2014 Aug 15;88(16):9072-85.

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News

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).

May 13, 2014

Chimera production release 1.9 is now available. See the release notes for new features since the 1.8 release series.

April 23, 2014

A production release candidate (version 1.9) is now available; please try it and report any problems. See the release notes for changes relative to the previous release.

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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

unmatched structures superimposed structures

Superimposing Structures

There are several ways to superimpose structures in Chimera:
•  MatchMaker performs a fit after automatically identifying which residues should be paired. Pairing uses both sequence and secondary structure, allowing similar structures to be superimposed even when their sequence similarity is low to undetectable.
The figure shows five distantly related proteins (pairwise sequence identities <25%) from the SCOP WD40 superfamily before and after MatchMaker superposition with default parameters.
•  Structures can be matched using a pre-existing sequence alignment.
•  The exact atoms to pair can be specified with the match command. This works on any type of structure, while the preceding methods apply only to peptide and nucleotide chains.
•  Structures can be superimposed manually by activating/deactivating them for motion and using the mouse.

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Gallery Sample

RNA Bases

Large ribosomal RNA is shown with individual bases depicted using solvent excluded molecular surfaces. Bases A, C, G, U are colored red, yellow, green, and blue. The surfaces were made with the Chimera multiscale tool in combination with the nucleic acid blobs plug-in. The image was raytraced using POVray.

Protein Data Bank model 1s72.

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