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UCSF Chimera is an interactive molecular modeling system that supports 3-D visualization of protein structures.It runs as an application on the user's computer. The UCSC Genome Browser provides links to launch Chimera as a helper application for proteins with solved structures deposited in PDB. Protein residues with non-synonymous SNPs identified by LS-SNP PDB are annotated in Chimera by the UCSC Browser for genome assemblies with LS-SNP PDB entries (currently human).
Links to Chimera are available in the "Protein Domain and Structure Information" section of the UCSC Genes details page when the gene is associated with a PDB structure. Residues with non-synonymous SNPs are colored gold and labeled with the dbSNP identifier. Additionally, for SNPs in LS-SNP PDB, links to Chimera are generated on the SNP details page with the residue associated with the selected SNP colored red, and the other non-synonymous SNP residues colored gold.
Chimera version 1.3 or newer must be installed locally on your computer from the Download Chimera page. To automatically launch Chimera from one of these links, it must be configured as a web browser helper application as described in the Chimera Web Data page.
IMPORTANT NOTE: The UCSC Genome Browser group is unable to provide support for installing or using UCSF Chimera. If you need help, please see the UCSF Chimera Documentation or inquire on the Chimera users discussion mailing list.