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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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News

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.

(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, 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

5 comparative models
Model List dialog

Chimera Interface to Modeller

Chimera provides a graphical interface to running the program Modeller, either locally or via a web service hosted by the UCSF RBVI. Two types of calculations are available:

  • Comparative (homology) modeling. Theoretical models of a protein target are generated using at least one known related template structure and a target-template sequence alignment. There are several ways to generate these inputs in Chimera. See also the Comparative Modeling tutorial.

  • Building parts of a protein without using a template. Missing segments can be built de novo, or existing segments refined by generating additional possible conformations.
Modeller is developed by the Sali Lab.

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Gallery Sample

Orexin Receptor Complex

The image shows the structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant, Protein Data Bank entry 4s0v. The drug is shown as spheres colored by element, and the receptor as ribbons with secondary structure elements rainbow-colored from blue at the N-terminus to red at the C-terminus. (More samples...)