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Recent Citations

Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas. Hu C, Almendros C et al. Nature. 2021 Oct 21;598(7881):515-520.

Structural basis of human transcription-DNA repair coupling. Kokic G, Wagner FR et al. Nature. 2021 Oct 14;598(7880):368-372.

The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes. Tran NH, Carter SD et al. Science. 2021 Oct 1;374(6563):52-57.

A practical guide to large-scale docking. Bender BJ, Gahbauer S et al. Nat Protoc. 2021 Oct;16(10):4799-4832.

The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes. Sakuragi T, Kanai R et al. Nat Struct Mol Biol. 2021 Oct;28(10):825-834.

(Previously featured citations...)

Chimera Search

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News

December 18, 2020

Chimera production release 1.15 is now available. See the release notes for what's new.

December 11, 2020

The RBVI wishes you a safe and happy holiday season! See our 2020 card and the gallery of previous cards back to 1985.

November 4, 2020

A 1.15 production release candidate is available, including a fix to work with the new PDB fetch locations (see the release notes). Please try it and report any problems.

(Previous news...)

Upcoming Events

November 9, 2021

SBGrid webinar 3pm PST Nov 9 (noon Nov 10 New Zealand time): Second speaker Tom Goddard (3:30pm) will show using AlphaFold-predicted structures for cryoEM modeling in ChimeraX [register for webinar].

UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. It is available free of charge for noncommercial use. Commercial users, please see Chimera commercial licensing.

We encourage Chimera users to try ChimeraX for much better performance with large structures, as well as other major advantages and completely new features. ChimeraX includes a significant subset of Chimera features (with more to come, see the missing features list) and is under active development. Users may choose to use both programs, and it is fine to have both installed.

Chimera is no longer under active development, and is only updated for critical maintenance. Chimera development was supported by a grant from the National Institutes of Health (P41-GM103311) that ended in 2018.

Feature Highlight

Ramachandran plot 1jfuA 1jfu chain A

Ramachandran Plot

Protein backbone angles can be shown in a Ramachandran Plot along with probability contours (green lines) from a reference set of well-determined structures. Each amino acid residue is shown as a dot in a graph of φ vs. ψ, more commonly known as a Ramachandran plot or Ramachandran map. Residues are shown as blue dots, or when selected, as red dots. In the example, all helix residues have been selected. Conversely, clicking a dot in the plot will select the corresponding residue in the structure. When the plot has mouse focus, the cursor position (x = φ, y = ψ) is reported under the plot.

(More features...)

Gallery Sample

Wasabi Receptor

The image shows the structure of the human TRPA1 ion channel (wasabi receptor) determined by electron cryo-microscopy, Protein Data Bank entry 3j9p. The four subunits of the tetramer are shown as ribbons in different colors over a dark-to-light gradient background. (More samples...)


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