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 licensing.

ChimeraX development is supported in part by grants from the National Institutes of Health (currently R01-GM129325, previously P41-GM103311).

Feature Highlight

Matchmaker Superposition

The matchmaker command is convenient for superimposing related structures without having to worry about numbering or missing residues. It superimposes proteins (and nucleic acids) by creating a pairwise sequence alignment, then matching the sequence-aligned residues in 3D. Secondary structure helps guide the sequence alignment for better performance on more distantly related proteins with harder-to-align sequences. By default, the fit is iterated to exclude structurally dissimilar regions and superimpose the most similar parts more closely.

The resulting sequence alignments can be displayed, as in this example of three pectate lyases: PDB 1jta, 1bn8, and 2pec. In the sequence alignments, residues used in the final fit iteration are enclosed in light orange boxes. RMSD values and other fit statistics are reported in the Log. For setup other than structure orientation, see the command file peclyases.cxc.

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Example Image

Potassium Channel-Calmodulin Complex

KCNQ1 is the pore-forming subunit of a cardiac potassium channel. It binds to calmodulin, and mutations in either of these proteins can cause congenital long QT syndrome, a dangerous propensity for irregular heartbeats. In the image, a structure of the KCNQ1/calmodulin complex (PDB 5vms) has been assembled into the native tetrameric form with the sym command. The view is from the cytoplasmic side, with KCNQ1 shown as surfaces, calmodulin as cartoons, and calcium ions as balls. A pastel palette from ColorBrewer has been used to color the surfaces, darkened with color modify for the cartoons, and “rotated” 45° in hue for the ions. See the command file colormod.cxc.

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