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:
RCSB Protein Data Bank (PDB)
Allows fetching structures in PDB and mmCIF formats by PDB ID. Also provides lookup of other PDB entry information by Blast Protein and PDB/UniProt Info.

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.

Modeller Comparative (Homology) Modeling
Chimera provides an interface for comparative modeling with Modeller, either run locally or using a Web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI).

Protein Quaternary Structure server
Allows fetching predicted biological units specified by PDB ID.

Allows fetching modeled organic molecule structures specified by PubChem CID from the Pub3D database. This database contains structures for millions of PubChem entries and is described in Willighagen et al., BMC Bioinformatics 8:487 (2007). Pub3D and the service for accessing it are provided by the CICC at Indiana University.

Generates modeled organic molecule structures specified by SMILES string with the command open or in Build Structure. The smi23d web service is provided by the CICC at Indiana University and deploys the same procedure used to populate Pub3D (above).
Density maps:
Electron Density Server
Allows fetching electron density maps (2fo-fc and fo-fc) specified by PDB ID.
Electron Microscopy Data Bank (EMDB)
Allows fetching electron density maps by EMDB identifier and finding maps by keyword search.
Other data or calculations:
BLAST Protein
The Blast Protein tool performs protein sequence searches using a BLAST Web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI).

Computed Atlas of Surface Topography of proteins (CASTp)
Allows fetching precomputed pocket measurements and corresponding structures specified by PDB ID.

The MultiFit tool performs simultaneous rigid fitting of multiple atomic-resolution structures into density maps using the program MultiFit (courtesy of Keren Lasker, Sali group) via a Web service hosted by the UCSF RBVI.

SaliLab Model Evaluation Server
Can be called to calculate additional scores for comparative models using the Fetch Scores menu in the Model List dialog.

Small-Angle X-Ray Profile
The Small-Angle X-Ray Profile tool calculates small-angle X-ray scattering (SAXS) profiles from structures using the program FoXS (courtesy of Dina Schneidman, Sali group) via a Web service hosted by the UCSF RBVI.

Used by Area/Volume from Web to calculate atomic surface areas (various methods) and Voronoi volumes from coordinates.

Allows fetching protein sequences and their feature annotations by UniProt ID, either for PDB structure chains by PDB/UniProt Info, or independent of structure.

2D Chemical Diagram
Used by Structure Diagram and ViewDock to draw 2D diagrams of small organic molecules given coordinates or a SMILES string. This Web service is implemented in Java using the Chemistry Development Kit and is provided by the UCSF RBVI.

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 (see screenshot and details).

UCSC Genome Browser
Chimera links are provided in UCSC Gene pages (see example) and SNP track details pages. Clicking a Chimera link displays the corresponding structure with nonsynonymous SNP residues colored and labeled with the dbSNP identifier.

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

MultiFit Webserver
The server performs simultaneous rigid fitting of multiple structures into a density map; clicking a thumbnail image in the results page opens the corresponding fitting solution in Chimera.

PhosphoSitePlus® (PSP)
Clicking "Get ChimeraX Script" on the Structure Viewer will show the structure in Chimera with experimentally observed sites of post-translational modification (PTM) colored and labeled. PSP is continuously updated with data on phosphorylation and other commonly studied PTMs.

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