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Featured Citations

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Croll TI. Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6).

Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule. Tsai JC, Miller-Vedam LE et al. Science. 2018 Mar 30;359(6383).

General prediction of peptide-MHC binding modes using incremental docking: A proof of concept. Antunes DA, Devaurs D et al. Sci Rep. 2018 Mar 12;8(1):4327.

Structure and conformational dynamics of the human spliceosomal Bact complex. Haselbach D, Komarov I et al. Cell. 2018 Jan 25;172(3):454-464.e11.

UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Goddard TD, Huang CC et al. Protein Sci. 2018 Jan;27(1):14-25.

See also: RCSB PDB Images
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News

April 6, 2018

ChimeraX version 0.6 is available. See the change log for what's new.

January 1, 2018

UCSF ChimeraX paper published in a special issue of Protein Science: Tools for Protein Science.

December 22, 2017

ChimeraX version 0.5 is available. See the change log for what's new.

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UCSF ChimeraX

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use. Commercial users, please see licensing.

ChimeraX development is supported in part by the National Institutes of Health (NIGMS P41-GM103311).

Feature Highlight

Stylized Nucleotides

Special representations of nucleotide sidechains can be shown with the nucleotides command. Options include slabs for bases (box, muffler, or ellipsoid shape), bumps on slabs to show base orientation, simple tubes instead of ribose atoms, and continuous or broken ladder rungs. Several possibilities are shown for a dGdC base pair in PDB 1bna (residues 22 and 3, respectively). Slabs are colored to match the nitrogen at one end of the glycosidic bond, tubes to match the ribose carbon (C1') at the other end, and ladder half-rungs to match the ribbon segment for the residue. Multiple nucleotide styles can be used within a single structure.

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Example Image

neuraminidase flowers

Potassium Channel-Calmodulin Complex

KCNQ1 is the pore-forming subunit of a cardiac potassium channel. It binds to calmodulin, and mutations in either of these proteins can cause congenital long QT syndrome, a dangerous propensity for irregular heartbeats. In the image, a structure of the KCNQ1/calmodulin complex (PDB 5vms) has been assembled into the native tetrameric form with the sym command. The view is from the cytoplasmic side, with KCNQ1 shown as surfaces, calmodulin as cartoons, and calcium ions as balls. A pastel palette from ColorBrewer has been used to color the surfaces, darkened with color modify for the cartoons, and “rotated” 45° in hue for the ions. See the command file colormod.cxc.

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