about projects people publications resources resources visit us visit us search search

Quick Links

Recent Citations

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.

Gastric proton pump with two occluded K+ engineered with sodium pump-mimetic mutations. Abe K, Yamamoto K et al. Nat Commun. 2021 Sep 29;12(1):5709.

Structural insights into the inhibition of undecaprenyl pyrophosphate synthase from Gram-positive bacteria. Workman SD, Day J et al. J Med Chem. 2021 Sep 23;64(18):13540-13550.

(Previously featured citations...)

Chimera Search

Google™ Search

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

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.

(More features...)

Gallery Sample

RNA Bases

Large ribosomal RNA is shown with individual bases depicted using solvent excluded molecular surfaces. Bases A, C, G, U are colored red, yellow, green, and blue. The surfaces were made with the Chimera multiscale tool in combination with the nucleic acid blobs plug-in. The image was raytraced using POVray.

Protein Data Bank model 1s72.

(More samples...)


About RBVI | Projects | People | Publications | Resources | Visit Us

Copyright 2018 Regents of the University of California. All rights reserved.