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.
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.
Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Chen M, Dai W et al. Nat Methods. 2017 Oct;14(10):983-985.
Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes. Fritz-Laylin LK, Riel-Mehan M et al. eLife. 2017 Sep 26;6. pii: e26990.See also: RCSB PDB Images
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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).
Several lighting modes are available, including ambient occlusion. The image shows hemoglobin (PDB 4hhb) with the four chains shown as surfaces of different colors and heme residues as spheres. The command lighting soft or the Graphics “sugar cube” icon can be used to turn on ambient shadowing from 64 directions. The command lighting gentle gives a similar result, except tuned to emphasize larger indentations.More features...
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.