Chimera connects to the following sites for data retrieval and calculations.
Atomic coordinates:Density maps:Protein Data Bank (PDB) Allows fetching structures (in PDB and mmCIF formats) by PDB ID.
Nucleic Acid Database (NDB) Translates NDB ID codes into PDB ID codes, which are then used to fetch structures from the PDB.
ASTRAL Compendium Allows fetching domain structures specified by SCOP domain identifier.
Virus Particle Explorer database Allows fetching icosahedral virus capsid structures (transformed into a standard orientation) specified by PDB ID.
ModBase Allows fetching modeled structures (comparative models) specified by SwissProt, TrEMBL, GenPept or PIR accession code.
Protein Quaternary Structure server Allows fetching predicted biological units specified by PDB ID.
Pub3D Allows fetching modeled organic molecule structures specified by PubChem CID (also accessed from Build Structure). The Pub3D database contains structures for millions of PubChem entries and is provided by the Chemical Informatics and Cyberinfrastructure Collaboratory (CICC) at Indiana University.
smi23d Generates modeled organic molecule structures specified by SMILES string with the command open or in Build Structure. The smi23d server is provided by the Chemical Informatics and Cyberinfrastructure Collaboratory (CICC) at Indiana University.
Other data or calculations:Electron Density Server Allows fetching electron density maps (2fo-fc and fo-fc) specified by PDB ID.
Computed Atlas of Surface Topography of proteins (CASTp) Allows fetching precomputed pocket measurements and corresponding structures specified by PDB ID.
StrucTools Used by Area/Volume from Web to calculate atomic surface areas (various methods) and Voronoi volumes from coordinates.
GIF Creator for Chemical Structures Used by Structure Diagram and ViewDock to draw 2D diagrams of small organic molecules given coordinates or a SMILES string. The web service is courtesy of Dr. W. D. Ihlenfeldt and hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics.