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Recent Citations

The pathway to GTPase activation of elongation factor SelB on the ribosome. Fischer N, Neumann P et al. Nature. 2016 Dec 1;540(7631):80-85.

Structure of RagB, a major immunodominant outer-membrane surface receptor antigen of Porphyromonas gingivalis. Goulas T, Garcia-Ferrer I et al. Mol Oral Microbiol. 2016 Dec;31(6):472-485.

Structure and function of the nuclear pore complex cytoplasmic mRNA export platform. Fernandez-Martinez J, Kim SJ et al. Cell. 2016 Nov 17;167(5):1215-1228.e25.

An HIV-1 antibody from an elite neutralizer implicates the fusion peptide as a site of vulnerability. van Gils MJ, van den Kerkhof TL et al. Nat Microbiol. 2016 Nov 14;2:16199.

Mechanisms of insertion of dCTP and dTTP opposite the DNA lesion O6-methyl-2'-deoxyguanosine by human DNA polymerase η. Patra A, Zhang Q et al. J Biol Chem. 2016 Nov 11;291(46):24304-24313.

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Chimera Search

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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.

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.

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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

density display

Density Display

Electron density maps can be read from local files or fetched from databases. Chimera's Volume Viewer allows adjusting contour levels interactively, showing multiple isosurfaces for a given map, and restricting display to a zone around selected atoms. The figure shows PDB entry 2fma and its electron density map. Settings are similar to those described in the Density Display tutorial. See also: Chimera volume display guide

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Gallery Sample

Loop Interactions

The image shows interactions of the delta-1 loop with the rest of hepatitis C virus RNA-dependent RNA polymerase (Protein Data Bank entry 1quv). Loop residues in contact with the rest of the structure (van der Waals overlap ≥ 0.01 Å) are displayed as sticks; interacting surface atoms are shown as red patches. (More samples...)