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Recent Citations

Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation. Wild R, Kowal J et al. Science. 2018 Feb 2;359(6375):545-550.

Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes. Poepsel S, Kasinath V, Nogales E. Nat Struct Mol Biol. 2018 Feb;25(2):154-162.

Structure and mutagenesis reveal essential capsid protein interactions for KSHV replication. Dai X, Gong D et al. Nature. 2018 Jan 25;553(7689):521-525.

A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. Korolev N, Lyubartsev AP, Nordenskiöld L. Sci Rep. 2018 Jan 24;8(1):1543.

A self-assembled nanoscale robotic arm controlled by electric fields. Kopperger E, List J et al. Science. 2018 Jan 19;359(6373):296-301.

(Previously featured citations...)

Chimera Search

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October 24, 2017

Chimera production release 1.12 is now available (64-bit builds for Windows, Mac, and Linux). See the release notes for details.

September 12, 2017

A production release candidate (version 1.12) is available; please try it and report any problems. See the release notes for what's new.

March 13, 2017

For a nice 3D-printing protocol that uses Chimera, see 3D Printing of Biomolecular Models for Research and Pedagogy by Da Veiga Beltrame, Tyrwhitt-Drake, et al. today in JoVE!

(Previous news...)

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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, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), funded by the National Institutes of Health (NIGMS P41-GM103311).

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the RBVI, following UCSF Chimera.

Feature Highlight

sidechain 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.

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Gallery Sample

Wasabi Receptor

The image shows the structure of the human TRPA1 ion channel (wasabi receptor) determined by electron cryo-microscopy, Protein Data Bank entry 3j9p. The four subunits of the tetramer are shown as ribbons in different colors over a dark-to-light gradient background. (More samples...)