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Recent Citations

Architecture of a transcribing-translating expressome. Kohler R, Mooney RA et al. Science. 2017 Apr 14;356(6334):194-197.

Mediator structure and rearrangements required for holoenzyme formation. Tsai KL, Yu X et al. Nature. 2017 Apr 13;544(7649):196-201.

PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation. Wu R, Sanishvili R et al. Proc Natl Acad Sci USA. 2017 Apr 11;114(15):3891-3896.

Structural, functional, and clinical characterization of a novel PTPN11 mutation cluster underlying Noonan syndrome. Pannone L, Bocchinfuso G et al. Hum Mutat. 2017 Apr;38(4):451-459.

Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. Praetorius F, Dietz H. Science. 2017 Mar 24;355(6331).

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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, nonprofit, 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.

Feature Highlight

sequence alignment structure

Sequence Viewer

The Multalign Viewer tool displays individual sequences and multiple sequence alignments. Sequence alignments can be read from external files (several formats) or created by other tools in Chimera. Structures opened in Chimera are automatically associated with sufficiently similar sequences in the alignment. After association,

  • mousing over a residue in the sequence shows its structure residue number
  • selecting in the sequence selects residues in the structure(s) and vice versa
  • structures can be superimposed using the sequence alignment
Various measures of sequence conservation and structural variation (RMSD) can be computed and shown above the sequences as histograms, and on the structures with color or worm radius. Secondary structure elements can be depicted as colored boxes or regions on the alignment. Regions can also be created by hand.

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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.

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