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

View Channels from MOLEonline

The MOLEonline Server calculates channels in protein structures and provides several types of analyses. Results can be downloaded in several different formats, including JSON.

A JSON file downloaded from the MOLEonline Server can be opened in ChimeraX version 1.5 and newer. A sphere model is generated for each channel in the file, and if the file contains more than one channel, a slider interface will appear for flipping through them one by one. Since the channels are individual models in ChimeraX, it is also easy to view more than one at the same time, change their colors, etc. using the Model Panel and/or commands. For image setup, see the command file 2dkh-mole.cxc and data file 2dkh-channels.json. See also the MOLE Channel Coloring by Property tutorial.

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Example Image

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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