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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 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases.
The example shows modeling the human (shades of blue) from the mouse (brown and tan) complex of programmed death-1 (PD-1) with its ligand PD-L2, PDB 3bp5.
Comparative modeling requires a template structure and a target-template sequence alignment for each unique chain. The sequences of human PD-1 and PD-L2 targets were fetched from UniProt and associated with the corresponding chains in the template structure, see model-pdl-setup.cxc. (Pairwise or multiple sequence alignments could have been used, but in this case, the template structure was simply associated with the target sequence.) Sequence-structure association shows mismatches in the Sequence Viewer: pink boxes for sequence differences between mouse and human, and gray outlines around the parts missing from the structure.
Three models were made with with default settings (other than the number of models), and the best-scoring model is shown. Two positions where sequence differences change the interfacial H-bonds are displayed.More features...
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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