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Recent Citations

Structure of a prehandover mammalian ribosomal SRP·SRP receptor targeting complex. Kobayashi K, Jomaa A et al. Science. 2018 Apr 20;360(6386):323-327.

Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes. Dai X, Zhou ZH. Science. 2018 Apr 6;360(6384). pii: eaao7298.

Structure of the insulin receptor-insulin complex by single-particle cryo-EM analysis. Scapin G, Dandey VP et al. Nature. 2018 Apr 5;556(7699):122-125.

Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule. Tsai JC, Miller-Vedam LE et al. Science. 2018 Mar 30;359(6383).

Binding of ISRIB reveals a regulatory site in the nucleotide exchange factor eIF2B. Zyryanova AF, Weis F et al. Science. 2018 Mar 30;359(6383):1533-1536.

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Chimera Search

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October 24, 2017

Chimera production release 1.12 is now available (64-bit builds for Windows, Mac, and Linux). See the release notes for details.

September 12, 2017

A production release candidate (version 1.12) is available; please try it and report any problems. See the release notes for what's new.

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!

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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 (NIGMS P41-GM103311).

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

Feature Highlight

Screening Docked Molecules

View Dock image

Given the structures of ligand and receptor molecules, docking programs calculate possible binding modes. In virtual screening, small organic compounds (typically from a database of many thousands) are treated as possible ligands, and a target macromolecule is treated as the receptor.

ViewDock facilitates the interactive selection of compounds from the output of docking programs, including DOCK and Maestro/Glide. The hits can be viewed in the context of the binding site and sorted or screened by various properties such as score or number of hydrogen bonds to the receptor. The Dock Prep tool can be used to prepare structures for docking or other calculations by adding hydrogens, assigning partial charges, and performing other related tasks.

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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...)