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Recent Citations

High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation. Mattei S, Tan A et al. Proc Natl Acad Sci USA. 2018 Oct 2;115(40):E9401-E9410.

Structural basis for activation of voltage sensor domains in an ion channel TPC1. Kintzer AF, Green EM et al. Proc Natl Acad Sci USA. 2018 Sep 25;115(39):E9095-E9104.

Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin. Hu J, Worrall LJ et al. Nat Commun. 2018 Sep 21;9(1):3840.

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA. Mishra S, Ahmed T et al. Sci Rep. 2018 Sep 11;8(1):13587.

Sub-2‚ÄČÅ Ewald curvature corrected structure of an AAV2 capsid variant. Tan YZ, Aiyer S et al. Nat Commun. 2018 Sep 7;9(1):3628.

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News

September 21, 2018

Mac users are advised to hold off upgrading to Mojave until we find a fix for Chimera buttons not being shown until the windows containing them are resized.

July 3, 2018

Chimera production release 1.13 is now available. See the release notes for what's new.

June 2, 2018

A production release candidate (version 1.13) is available; please try it and report any problems. See the release notes for what's new.

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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, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), supported in part by the National Institutes of Health (P41-GM103311).

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the RBVI, following UCSF Chimera.

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

Peroxiredoxin Wreath

Peroxiredoxins are enzymes that help cells cope with stressors such as high levels of reactive oxygen species. The image shows a decameric peroxiredoxin from human red blood cells (Protein Data Bank entry 1qmv), styled as a holiday wreath.

See also the RBVI holiday card gallery.

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