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Recent Citations

A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. Kazlauskiene M, Kostiuk G et al. Science. 2017 Aug 11;357(6351):605-609.

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Ou HD, Phan S et al. Science. 2017 Jul 28;357(6349):eaag0025.

Capturing protein communities by structural proteomics in a thermophilic eukaryote. Kastritis PL, O'Reilly FJ et al. Mol Syst Biol. 2017 Jul 25;13(7):936.

Ratchet-like polypeptide translocation mechanism of the AAA+ disaggregase Hsp104. Gates SN, Yokom AL et al. Science. 2017 Jul 21;357(6348):273-279.

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors. Serra F, Baù D et al. PLoS Comput Biol. 2017 Jul 19;13(7):e1005665.

(Previously featured citations...)

Chimera Search

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March 13, 2017

For a nice 3D-printing protocol that uses Chimera, see 3D Printing of Biomolecular Models for Research and Pedagogy by Da Veiga Beltrame, Tyrwhitt-Drake, et al. today in JoVE!

December 2, 2016

Chimera production release 1.11.2 is now available. This version has been updated to work with changes in NCBI Blast and to avoid crashes on Mac Sierra (see the release notes for details).

September 24, 2016

Production release candidate (version 1.11.2) is available, superseding 1.11.1. The new version has been updated to work with changes in NCBI Blast (see release notes). Please try it and report any problems.

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

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

Feature Highlight

RR Distance Maps 2gbp and 2fw0

Distance Maps and Contact Maps

RR Distance Maps creates a distance map, a generalization of a protein contact map in which residue-residue distances are shown with color gradations. The map can show the Cα-Cα distances within an individual protein chain or the averages and standard deviations for multiple related chains (as in the figure). A simple binary coloring like a standard contact map can also be obtained.

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Gallery Sample

Binding Site Similarity

β-1,4-glycanase (gold, PDB 1exp) and cellobiohydrolase I (cyan, PDB 1cel) have similar glucose-binding sites but different folds. Ribbons were slimmed with Ribbon Style Editor and the title and captions were added with 2D Labels (see image how-to). (More samples...)