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Recent Citations

Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli. Jackson RN, Golden SM et al. Science. 2014 Sep 19;345(6203):1473-9.

Molecular architecture and mechanism of the anaphase-promoting complex. Chang L, Zhang Z et al. Nature. 2014 Sep 18;513(7518):388-93.

Spatial localization of the Ebola virus glycoprotein mucin-like domain determined by cryo-electron tomography. Tran EE, Simmons JA et al. J Virol. 2014 Sep 15;88(18):10958-62.

A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. McHugh CA, Fontana J et al. EMBO J. 2014 Sep 1;33(17):1896-911.

A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Geary C, Rothemund PW, Andersen ES. Science. 2014 Aug 15;345(6198):799-804.

(Previously featured citations...)

Chimera Search

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News

August 15, 2014

We are delighted to announce the publication of a new book, Computational and Visualization Techniques for Structural Bioinformatics Using Chimera, written by Forbes J. Burkowski (University of Waterloo).

May 13, 2014

Chimera production release 1.9 is now available. See the release notes for new features since the 1.8 release series.

April 23, 2014

A production release candidate (version 1.9) is now available; please try it and report any problems. See the release notes for changes relative to the previous release.

(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, funded by the National Institutes of Health (NIGMS P41-GM103311).

Feature Highlight

Blast Protein

The Blast Protein tool performs a blast or psiblast search of pdb or nr for sequences similar to a query, using a Web service hosted by the UCSF RBVI. The query can be:

  • a chain from a structure open in Chimera
  • a sequence pasted as plain text
  • a sequence from an alignment in Multalign Viewer
The output is a list of hits, from which all or a user-chosen subset can be retrieved:
  • as a pseudo-multiple sequence alignment (a consolidation of the pairwise alignments of individual hits to the query), automatically shown in Multalign Viewer
  • as structures (for hits from pdb), automatically superimposed according to the pseudo-multiple alignment

(More features...)

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...)