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Recent Citations

Global computational mutagenesis of domain structures associated with inherited eye disease. Ortiz FW, Sergeev YV. Sci Rep. 2019 Mar 6;9(1):3676.

Cryo-EM of retinoschisin branched networks suggests an intercellular adhesive scaffold in the retina. Heymann JB, Vijayasarathy C et al. J Cell Biol. 2019 Mar 4;218(3):1027-1038.

Assessing the predictive power of relative binding free energy calculations for test cases involving displacement of binding site water molecules. Wahl J, Smieško M. J Chem Inf Model. 2019 Feb 25;59(2):754-765.

Circadian oscillator proteins across the kingdoms of life: structural aspects. Saini R, Jaskolski M, Davis SJ. BMC Biol. 2019 Feb 18;17(1):13.

CasX enzymes comprise a distinct family of RNA-guided genome editors. Liu JJ, Orlova N et al. Nature. 2019 Feb 14;566(7743):218-223.

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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.

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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), 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

dopamine receptor with axes and planes

Axes and Planes

Axes, planes, and centroids can be calculated from sets of atoms using the Axes/Planes/Centroids tool or the command define. Axes can be shown as cylinders, planes as disks, and centroids as spheres, and any of these can be used in distance and angle measurements.

For example, the figure shows the dopamine D3 receptor and bound inhibitor (PDB entry 3pbl) as modeled into the membrane in the OPM database. The planes of the inner and outer membrane boundaries are shown as transparent blue and red disks, respectively. The protein ribbon is rainbow-colored from blue at the N-terminus to red at the C-terminus, and the axis of each helix is shown as a cylinder of matching color. The axis of the red helix forms an angle of 15.1° with the membrane and comes within 3.5 Å of the inner boundary. The yellow and orange helices are nearly antiparallel (crossing angle 5.9°). The average (minimum, maximum) distance of inhibitor atoms from the outer boundary is 7.9 (5.1, 11.7) Å.

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Gallery Sample

Binding Site Similarity

β-1,4-glycanase (gold, PDB 1exp) and cellobiohydrolase I (cyan, PDB 1cel) have similar glucose-binding sites but different folds. Ribbons were slimmed with Ribbon Style Editor and the title and captions were added with 2D Labels (see image how-to). (More samples...)

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