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.

ChimeraX on Bluesky: @chimerax.ucsf.edu

Feature Highlight

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.

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Example Image

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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