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Recent Citations

Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Laughlin TG, Deep A et al. Nature. 2022 Aug 11;608(7922):429-435.

Implementation of occupied and virtual Edmiston-Ruedenberg orbitals using Cholesky decomposed integrals. Folkestad SD, Matveeva R et al. J Chem Theory Comput. 2022 Aug 9;18(8):4733-4744.

Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. Boninsegna L, Yildirim A et al. Nat Methods. 2022 Aug;19(8):938-949.

Membrane-anchored HDCR nanowires drive hydrogen-powered CO2 fixation. Dietrich HM, Righetto RD et al. Nature. 2022 Jul 28;607(7920):823-830.

Fusion protein strategies for cryo-EM study of G protein-coupled receptors. Zhang K, Wu H et al. Nat Commun. 2022 Jul 28;13(1):4366.

(Previously featured citations...)

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News

December 20, 2021

The RBVI wishes you a safe and happy holiday season! See our 2021 card and the gallery of previous cards back to 1985.

December 17, 2021

Chimera production release 1.16 is now available. This will be the last release to support Windows 7. See the release notes for what's new.

December 18, 2020

Chimera production release 1.15 is now available. See the release notes for what's new.

(Previous news...)

Upcoming Events

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

sidechain rotamers

Rotamers

Amino acid sidechains adopt different conformational states, or rotamers. Rotamers from the Dunbrack backbone-dependent library or the Richardson "penultimate" library can be viewed, evaluated, and incorporated into structures with the Rotamers tool. A residue can be changed into a different conformation of the same type of amino acid or mutated into a different type. Rotamer torsion angles and library probability values are listed in a dialog, along with (optionally) hydrogen bonds, clashes, and agreement with electron density data. Only rotamers chosen in the list are displayed. When a single rotamer is chosen, it can be incorporated into the structure. The image includes 2D labels.

(More features...)

Gallery Sample

Annotated Green Fluorescent Protein

BILD format was used in Chimera to annotate the barrel structure of green fluorescent protein with its centroid, major axis (red arrow), and an enclosing cylinder (shown with green hoops). The BILD file green.bild was generated with the python program green.py using the coordinates in green.pdb. Gallery entry courtesy of Mike Ess, Yeast Resource Center, University of Washington. (More samples...)


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