Web Services Used by UCSF Chimera

Chimera connects to the following sites for data retrieval and calculations. See also: sites that provide Chimera Web data

Atomic coordinates:
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.

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.

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.

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.
Density maps:
Electron Density Server
Allows fetching electron density maps (2fo-fc and fo-fc) specified by PDB ID.
Other data or calculations:
Computed Atlas of Surface Topography of proteins (CASTp)
Allows fetching precomputed pocket measurements and corresponding structures specified by PDB ID.

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 (see usage conditions) and hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics.

Sites That Provide Chimera Web Data

Accessing Chimera Web data (such as by clicking a link or choosing a display option at one of these sites) automatically displays database contents or server results in a locally installed copy of Chimera.

The ConSurf Server
Clicking the link to view results in Chimera displays the query structure and the multiple sequence alignment from ConSurf, both colored by the server's conservation measure. The ConSurf-calculated phylogenetic tree and custom headers are shown along with the sequence alignment.

Choosing the "launch Chimera" option to show a modeled structure displays it along with the template structure and their pairwise sequence alignment.

The Structure-Function Linkage Database
Chimera Web data files are provided for viewing enzyme structures, active sites (Chimera sessions), and sequence alignments.