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Featured Citations

ArtiaX: An electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX. Ermel UH, Arghittu SM, Frangakis AS. Protein Sci. 2022 Dec;31(12):e4472.

Structural principles of B cell antigen receptor assembly. Dong Y, Pi X et al. Nature. 2022 Dec 1;612(7938):156–161.

Starting a new chapter on class Ia ribonucleotide reductases. Levitz TS, Drennan CL. Curr Opin Struct Biol. 2022 Dec;77:102489.

Structural basis for mechanotransduction in a potassium-dependent mechanosensitive ion channel. Mount J, Maksaev G et al. Nat Commun. 2022 Nov 12;13(1):6904.

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

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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

1g74 per-model clipping

Per-Model Clipping

Front/back (rotatable) clipping can be applied selectively to some models but not others. This is most often used to slice a molecular surface but not the corresponding atomic structure.

For example, the protein in PDB entry 1g74 has an oleic acid residue OLA in an interior pocket. The script in pmc.cxc shows the protein surface, activates front clipping for all models, and then turns it off for just the atomic model, as shown in the figure. The clipping plane can be translated and rotated interactively with the mouse .

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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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