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Defining variant-resistant epitopes targeted by SARS-CoV-2 antibodies: A global consortium study. Hastie KM, Li H et al. Science. 2021 Oct 22;374(6566):eabh2315.

Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies. Lempp FA, Soriaga LB et al. Nature. 2021 Oct 14;598(7880):342-347.

Reconstitution of an intact clock reveals mechanisms of circadian timekeeping. Chavan AG, Swan JA et al. Science. 2021 Oct 8;374(6564):eabd4453.

Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism. Rao Q, Han L et al. Nat Struct Mol Biol. 2021 Oct;28(10):799-810.

Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. Zhang K, Julius D, Cheng Y. Cell. 2021 Sep 30;184(20):5138-5150.e12.

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News

May 28, 2021

The ChimeraX 1.2 production release is available. See the change log for what's new.

December 11, 2020

The RBVI wishes you a safe and happy holiday season! See our 2020 card and the gallery of previous cards back to 1985.

November 4, 2020

New paper online: UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Pettersen EF, Goddard TD, et al. Protein Sci. 2020, in press.

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Upcoming Events

November 9, 2021

SBGrid webinar 3pm PST Nov 9 (noon Nov 10 New Zealand time): Second speaker Tom Goddard (3:30pm) will show using AlphaFold-predicted structures for cryoEM modeling in ChimeraX [register for webinar].


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 ChimeraX commercial licensing.

ChimeraX is developed with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases.

Feature Highlight

THRβ and binding-site rotamers rotamer list dialog

Rotamers and Swapaa Virtual Mutation

Rotamers is an interface for showing amino acid sidechain rotamers and optionally replacing the original sidechain, also implemented as the swapaa command. The rotamers can be shown all at once, as in the figure, or individually by choosing rows in the dialog.

The figure shows binding-site residues of the thyroid hormone receptor β with hormone bound, PDB 3gws. Rotamers for the hormone-resistance mutations N331H and L346R are shown as partially transparent sticks, with H-bonds (light blue dashed line) and clashes (light purple dashed lines) calculated for the histidine rotamers at position 331. The rotamer-list dialog for this position is also shown. Command script rotamers.cxc contains the initial, noninteractive part of the setup.

These mutations are described in Cardoso et al., Endocrine (2020). Although one histidine rotamer may be able to form the same pocket-stabilizing H-bond as the wild-type asparagine, it also clashes with several atoms (third row in the dialog). H-bonds and clashes are not shown for the arginine rotamers at 346, but they all clash significantly with the hormone and/or other pocket atoms.

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Example Image

CaM-CaMKI peptide

Calmodulin and Target Peptide

Calmodulin (CaM) acts as a calcium sensor. When its four Ca++ sites are fully occupied, it binds and modulates the activity of various downstream proteins, including CaM-dependent protein kinase I (CaMKI). Here, a complex between CaM and its target peptide from CaMKI (PDB 1mxe) is shown with cartoons, a transparent molecular surface, silhouette outlines, and light soft ambient occlusion. (If you prefer a less smudgy/rustic appearance, try using light gentle instead.) For image setup other than positioning, see the command file cam.cxc.

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