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Recent Citations

Continuous Evaluation of Ligand Protein Predictions: A weekly community challenge for drug docking. Wagner JR, Churas CP et al. Structure. 2019 Aug 6;27(8):1326-1335.e4.

A visualization tool for cryo-EM protein validation with an unsupervised machine learning model in Chimera platform. Chen L, Baker B et al. Medicines. 2019 Aug 6; 6(3):86.

Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Twomey EC, Ji Z et al. Science. 2019 Aug 2;365(6452). pii: eaax1033.

Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Cooney I, Han H et al. Science. 2019 Aug 2;365(6452):502-505.

The pigment-protein network of a diatom photosystem II-light-harvesting antenna supercomplex. Pi X, Zhao S et al. Science. 2019 Aug 2;365(6452). pii: eaax4406.

(Previously featured citations...)

Chimera Search

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November 17, 2018

Chimera production release 1.13.1 is now available; see the release notes for what's new. The Mac version requires OS 10.10 or later.

October 22, 2018

Mac users: the 1.13.1 release candidate and recent daily builds contain a fix for Mojave (OS 10.14). These versions require OS 10.10 or later.

September 21, 2018

Mac users are advised to hold off upgrading to Mojave until we find a fix for Chimera buttons not being shown until the windows containing them are resized.

(Previous news...)

Upcoming Events

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), supported in part by the National Institutes of Health (P41-GM103311).

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

Feature Highlight

RR Distance Maps 2gbp and 2fw0

Distance Maps and Contact Maps

RR Distance Maps creates a distance map, a generalization of a protein contact map in which residue-residue distances are shown with color gradations. The map can show the Cα-Cα distances within an individual protein chain or the averages and standard deviations for multiple related chains (as in the figure). A simple binary coloring like a standard contact map can also be obtained.

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Gallery Sample

Orexin Receptor Complex

The image shows the structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant, Protein Data Bank entry 4s0v. The drug is shown as spheres colored by element, and the receptor as ribbons with secondary structure elements rainbow-colored from blue at the N-terminus to red at the C-terminus. (More samples...)

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