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Recent Citations

Structural and biochemical characterization of AidC, a quorum-quenching lactonase with atypical selectivity. Mascarenhas R, Thomas PW et al. Biochemistry. 2015 Jul 21;54(28):4342-53.

A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly. Dodonova SO, Diestelkoetter-Bachert P et al. Science. 2015 Jul 10;349(6244):195-198.

Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers. Fibriansah G, Ibarra KD et al. Science. 2015 Jul 3;349(6243):88-91.

The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Nguyen TH, Galej WP et al. Nature. 2015 Jul 2;523(7558):47-52.

Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles. Bharat TA, Murshudov GN et al. Nature. 2015 Jul 2;523(7558):106-10.

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News

July 23, 2015

Chimera production release 1.10.2 is now available. Fixes include code signing for Mac OS X installation. The 1.10 series will be the last to support OS X 10.6 and 10.7. See the release notes for details.

January 9, 2015

Chimera production release 1.10.1 is now available. 64-bit builds are recommended for all capable platforms, and the 1.10 series will be the last to support OS X 10.6 and 10.7. See the release notes for details.

November 5, 2014

Chimera production release 1.10 is now available. 64-bit builds are recommended for all capable platforms, and v1.10 will be the last to support OS X 10.6 and 10.7. See the release notes for what's new.

(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

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

Cavity and Tunnel Detection

Side-by-side views of a potassium channel structure (Protein Data Bank entry 1bl8) showing different approaches to cavity detection. On the left are molecular surface patches corresponding to the structure's two largest pockets by MS volume in the Computed Atlas of Surface Topography of proteins (CASTp) database. On the right is a tunnel in blue identified by the MolAxis server. Simple editing converted MolAxis output into a BILD file for display in Chimera. (More samples...)