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Cryo-EM structure of the SEA complex. Tafur L, Hinterndorfer K et al. Nature. 2022 Nov 10;611(7935):399–404.

Structural basis of actin filament assembly and aging. Oosterheert W, Klink BU et al. Nature. 2022 Nov 10;611(7935):374–379.

Molecular glue CELMoD compounds are regulators of cereblon conformation. Watson ER, Novick S et al. Science. 2022 Nov 4;378(6619):549-553.

Mechanism of an intramembrane chaperone for multipass membrane proteins. Smalinskaitė L, Kim MK et al. Nature. 2022 Nov 3;611(7934):161-166.

Dual targeting factors are required for LXG toxin export by the bacterial type VIIb secretion system. Klein TA, Grebenc DW et al. mBio. 2022 Oct 26;13(5):e0213722.

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News

November 23, 2022

The ChimeraX 1.5 production release is available! See the change log for what's new.

October 13, 2022

The ChimeraX 1.5 release candidate is available! Please try it and report any issues. See the change log for what's new.

September 27, 2022

Website downtime: The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tue, Sep 27 9pm PDT, through Wed, possibly extending to Thu, Sep 29 5pm PDT.

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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 ChimeraX commercial licensing.

ChimeraX is developed with support from National Institutes of Health R01-GM129325, Chan Zuckerberg Initiative grant EOSS4-0000000439, 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

HIV-1 protease B-factor coloring

B-factor Coloring

Atomic B-factor values are read from PDB and mmCIF input files and assigned as attributes that can be shown with coloring and used in atom specification. This example shows B-factor variation within a structure of the HIV-1 protease bound to an inhibitor (PDB 4hvp). For complete image setup, including positioning, color key, and label, see the command file bfactor.cxc.

Additional color key examples can be found in tutorials: Coloring by Electrostatic Potential, Coloring by Sequence Conservation

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