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Recent Citations

Structural basis of amine odorant perception by a mammal olfactory receptor. Guo L, Cheng J et al. Nature. 2023 Jun 1;618(7963):193–200.

Ligand and G-protein selectivity in the κ-opioid receptor. Han J, Zhang J et al. Nature. 2023 May 11;617(7960):417-425.

MELD-Bracket ranks binding affinities of diverse sets of ligands. Parui S, Robertson JC et al. J Chem Inf Model. 2023 May 8;63(9):2857-2865.

Molecular basis of translation termination at noncanonical stop codons in human mitochondria. Saurer M, Leibundgut M et al. Science. 2023 May 5;380(6644):531-536.

Structural basis of BAM-mediated outer membrane β-barrel protein assembly. Shen C, Chang S et al. Nature. 2023 May 4;617(7959):85–193.

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April 19, 2023

Chimera production release 1.17.1 is now available, fixing an issue with 1.17 for Windows and Linux. See the release notes for details.

April 13, 2023

Chimera production release 1.17 is now available. Updating is required to keep using the tools that run Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE, as these will soon stop working in older versions. See the release notes for details.

December 21, 2022

The RBVI wishes you a safe and happy holiday season! See our 2022 card and the gallery of previous cards back to 1985.

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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

structure-based sequence alignment superimposed structures

Structure-Based Sequence Alignment

Given two or more superimposed structures, Match→Align creates a corresponding sequence alignment. The user specifies a distance cutoff for residues allowed to be in the same column of the output alignment. In proteins, the distances are measured between α-carbons. The method is independent of residue types and how the structures were superimposed.
The figure shows a superposition from MatchMaker of five proteins from the SCOP WD40 superfamily and a corresponding sequence alignment from Match→Align, automatically shown in Multalign Viewer. In the sequence alignment, light green and yellow boxes indicate strands and helices, while the headers RMSD and Conservation show spatial and sequence conservation, respectively.

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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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