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Recent Citations

Molecular architecture of the Saccharomyces cerevisiae activated spliceosome. Rauhut R, Fabrizio P et al. Science. 2016 Sep 23;353(6306):1399-405.

The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface. Wurm JP, Overbeck J, Sprangers R. RNA. 2016 Sep;22(9):1360-72.

Spiral architecture of the Hsp104 disaggregase reveals the basis for polypeptide translocation. Yokom AL, Gates SN et al. Nat Struct Mol Biol. 2016 Sep;23(9):830-7.

Cryo-EM structure of a tetrameric cyanobacterial photosystem I complex reveals novel subunit interactions. Semchonok DA, Li M et al. Biochim Biophys Acta. 2016 Sep;1857(9):1619-26.

Structure of the STRA6 receptor for retinol uptake. Chen Y, Clarke OB et al. Science. 2016 Aug 26;353(6302):aad8266.

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Chimera Search

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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.

August 27, 2016

A production release candidate (version 1.11.1) is now available. Please try it and report any problems. See the release notes for what's been fixed since 1.11. The 1.11 release series will be the last to support 32-bit builds.

July 15, 2016

Chimera production release 1.11 is now available. 64-bit builds are now recommended for all capable platforms, and v1.11 will be the last to support 32-bit builds. See the release notes for details.

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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 (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. It is in early development and not yet publicly released, with release anticipated sometime in 2016.

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

Sliced Potassium Channel

Potassium channel (Protein Data Bank entry 1bl8) on a dark slate blue background with potassium ions shown in firebrick. The channel is comprised of four chains. Each chain has been rainbow-colored from blue at the N-terminus to red at the C-terminus, but only the surface of the channel is shown. The surface has been sliced with a per-model clipping plane. The surface cap color is plum except with opacity set to 0.8. The shininess and brightness have been set to 128 and 8, respectively, and the lights on the scene have been moved from their default positions. The subdivision quality (related to the smoothness of the spherical ions) is 5.0, and the molecular surface was computed with probe radius and vertex density set to 1.0 and 6.0, respectively. (More samples...)