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Recent Citations

A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure. Bonilla SL, Sherlock ME et al. Science. 2021 Nov 19;374(6570):955-960.

AKIRIN2 controls the nuclear import of proteasomes in vertebrates. de Almeida M, Hinterndorfer M et al. Nature. 2021 Nov 18;599(7885):491-496.

Dispatched uses Na+ flux to power release of lipid-modified Hedgehog. Wang Q, Asarnow DE et al. Nature. 2021 Nov 11;599(7884):320-324.

Kainate receptor modulation by NETO2. He L, Sun J et al. Nature. 2021 Nov 11;599(7884):325-329.

Mapping the catalytic conformations of an assembly-line polyketide synthase module. Cogan DP, Zhang K et al. Science. 2021 Nov 5;374(6568):729-734.

(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

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

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

Peroxiredoxin Wreath

Peroxiredoxins are enzymes that help cells cope with stressors such as high levels of reactive oxygen species. The image shows a decameric peroxiredoxin from human red blood cells (Protein Data Bank entry 1qmv), styled as a holiday wreath.

See also the RBVI holiday card gallery.

(More samples...)


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