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Featured Citations

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.

Automating tasks in protein structure determination with the clipper python module. McNicholas S, Croll T et al. Protein Sci. 2018 Jan;27(1):207-216.

Molecular structure of human KATP in complex with ATP and ADP. Lee KPK, Chen J, MacKinnon R. eLife. 2017 Dec 29;6. pii: e32481.

Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Walls AC, Tortorici MA et al. Proc Natl Acad Sci USA. 2017 Oct 17;114(42):11157-11162.

See also: RCSB PDB Images
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News

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.

November 9, 2017

A fourth alpha release is available. See the change log for salient changes and when they occurred.

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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 funded by the National Institutes of Health (NIGMS P41-GM103311).

Feature Highlight

2ptt interchain H-bonds screenshot

Interactive H-Bond Histogram

Hydrogen bonds (H-bonds) can be identified with the command hbonds and plotted as an interactive histogram with the command crosslinks histogram.

The ChimeraX graphics window shows the complex between a natural killer cell receptor 2B4 and its ligand CD48 (PDB 2ptt). The receptor protein is blue, the ligand protein pink, and H-bonds between them dashed yellow, with H-bonding residues labeled. Although not done here, the H-bonds could also be labeled by distance.

The histogram of H-bond distances on the top right is interactive: when the cursor is placed over a bar in the histogram, the corresponding H-bonds are temporarily enlarged in the 3D view and the others hidden. For image setup other than orientation, see the command file hb3.cxc.

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Example Image

transducin switch regions

G-Protein Switch Regions

The GDP- and GTP-bound conformations of the transducin α-subunit (1tag and 1tnd, respectively) differ primarily in three regions, termed switch 1, switch 2, and switch 3. The structures have been superimposed with matchmaker and shown as cartoons, with “empty” outlines where the structures are almost the same (for simplicity, only one conformation's outlines are shown). The GTP analog GTPγS is displayed as spheres color-coded by heteroatom. For 2D labels and image setup other than structure orientation, see the command file switch.cxc.

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