about projects people publications resources resources visit us visit us search search

Quick Links

Featured Citations

The Virtual Lab of AI agents designs new SARS-CoV-2 nanobodies. Swanson K, Wu W et al. Nature. 2025 Oct 16;646(8085):716–723.

Structural basis for the dynamic regulation of mTORC1 by amino acids. Valenstein ML, Wranik M et al. Nature. 2025 Oct 9;646(8084):493–500.

One-shot design of functional protein binders with BindCraft. Pacesa M, Nickel L et al. Nature. 2025 Oct 9;646(8084):483–492.

A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2. Vollmer B, Ebel H et al. Nature. 2025 Oct 9;646(8084):433–441.

A novel bacterial protein family that catalyses nitrous oxide reduction. He G, Wang W et al. Nature. 2025 Oct 2;646(8083):152–160.

More citations...

News

July 24, 2025

ChimeraX 1.10.1 is now available, fixing the problem in 1.10 of repeat registration requests to some users.

June 26, 2025

The ChimeraX 1.10 production release is available! See the change log for what's new.

May 7, 2025

The ChimeraX 1.10 release candidate is available – please try it and report any issues. See the change log for what's new.

Previous news...

Upcoming Events


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.

Bluesky logo ChimeraX on Bluesky: @chimerax.ucsf.edu

Feature Highlight

2gbp kvfinder cavities

Find Cavities

Pockets and cavities in protein structures can be identified with the Find Cavities tool or kvfinder command. These run KVFinder, a method based on surface shape developed by the Lopes-de-Oliveira group at the Brazilian Biosciences National Laboratory (details...).

As shown in the figure, the results are listed in an interactive cavity list and can be displayed as dot clouds and/or surfaces.

The latest iteration of this feature is available in ChimeraX 1.10 daily builds 4/17/25 and newer. For image setup other than position and the specific cavity colors (which are assigned randomly after a calculation), see the command file kvfinder.cxc.

More features...

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

More images...



About RBVI | Projects | People | Publications | Resources | Visit Us

Copyright 2018 Regents of the University of California. All rights reserved.