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

Quick Links

Recent Citations

A MERS-CoV-like mink coronavirus uses ACE2 as an entry receptor. Wang N, Ji W et al. Nature. 2025 Jun 19;642(8068):739–746.

Cryo-EM reveals structural diversity in prolate-headed mycobacteriophage Mycofy1. Li X, Shao Q et al. J Mol Biol. 2025 Jun 15;437(12):169126.

Conformational cycle and small-molecule inhibition mechanism of a plant ABCB transporter in lipid membranes. Liu Y, Liao M. Sci Adv. 2025 Jun 13;11(24):eadv9721.

Cat1 forms filament networks to degrade NAD+ during the type III CRISPR-Cas antiviral response. Baca CF, Majumder P et al. Science. 2025 Jun 12;388(6752):eadv9045.

Swinging lever mechanism of myosin directly shown by time-resolved cryo-EM. Klebl DP, McMillan SN et al. Nature. 2025 Jun 12;642(8067):519–526.

Previously featured citations...

Chimera Search

Google™ Search

News

March 6, 2025

Chimera production release 1.19 is now available, fixing the ability to fetch structures from the PDB (details...).

December 25, 2024

The RBVI wishes you a safe and happy holiday season! See our 2024 card and the gallery of previous cards back to 1985.

October 14, 2024

Planned downtime: The Chimera and ChimeraX websites, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable starting Monday, Oct 14 10 AM PDT, continuing throughout the week and potentially the weekend (Oct 14-20).

Previous news...

Upcoming Events

Please note that UCSF Chimera is legacy software that is no longer being developed or supported. Users are strongly encouraged to try UCSF ChimeraX, which is under active development.

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 in addition to nearly all the capabilities of Chimera (details...).

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

Feature Highlight

unmatched structures superimposed structures

Superimposing Structures

There are several ways to superimpose structures in Chimera:
•  MatchMaker performs a fit after automatically identifying which residues should be paired. Pairing uses both sequence and secondary structure, allowing similar structures to be superimposed even when their sequence similarity is low to undetectable.
The figure shows five distantly related proteins (pairwise sequence identities <25%) from the SCOP WD40 superfamily before and after MatchMaker superposition with default parameters.
•  Structures can be matched using a pre-existing sequence alignment.
•  The exact atoms to pair can be specified with the match command. This works on any type of structure, while the preceding methods apply only to peptide and nucleotide chains.
•  Structures can be superimposed manually by activating/deactivating them for motion and using the mouse.

(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.