Fetch by ID

Files can be retrieved from various databases and opened in Chimera with File... Fetch by ID. Internet connectivity is required to fetch files over the Web. The command open can also fetch files by ID.

A database and corresponding identifier (ID code) must be indicated:

• NDB - a Nucleic Acid Database identifier will be translated into a PDB ID and used to fetch a PDB-format file from the Protein Data Bank
• PDB - a 4-character PDB ID will be used to fetch a PDB-format file from the Protein Data Bank:
  1. Chimera will first attempt to find the file within a local installation of the Protein Data Bank. The default places to look for a local installation are /usr/mol/pdb/ and then /mol/pdb/ — these can be changed by editing the Python file share/chimera/pdbDir within a Chimera installation.
  2. If the file is not found locally, Chimera will try to retrieve it from the Protein Data Bank web site (by default; this can be turned off in the PDB preferences).
• PDB (mmCIF) - a 4-character PDB ID will be used to fetch an mmCIF-format file from the Protein Data Bank
• SCOP - a 7-character SCOP domain identifier will be used to fetch a PDB-format domain file from the ASTRAL Compendium
• PubChem - a PubChem compound identifier (CID) will be used to fetch a 3D structure (SDF) from the Pub3D database provided by the Chemical Informatics and Cyberinfrastructure Collaboratory (CICC) at Indiana University
• CASTp - a 4-character PDB ID (with chain ID optionally appended, for example 2gsh.A) will be used to fetch a structure and its precomputed pocket measurements from the Computed Atlas of Surface Topography of proteins (does not include results for all PDB entries; measurements will be displayed in a pocket list)
• EDS (2fo-fc) - a 4-character PDB ID will be used to fetch an electron density map from the Electron Density Server (not all PDB entries have maps available; Volume Viewer will be used to show the map)
• EDS (fo-fc) - a 4-character PDB ID will be used to fetch an electron density difference map from the Electron Density Server (not all PDB entries have maps available; Volume Viewer will be used to show the map)
• PQS - a 4-character PDB ID will be used to fetch the predicted biological unit from the Protein Quaternary Structure server (predictions are not available for all PDB entries; some entries have multiple predictions, and for those, multiple files will be retrieved)
• ModBase - a SwissProt, TrEMBL, GenPept or PIR accession code will be used to fetch comparative models in PDB format from ModBase (associated information will be shown in a model list)
• VIPERdb - an identifier in the Virus Particle Explorer database of icosahedral virus capsid structures will be used to fetch a PDB-format file from that database (the capsid will be constructed automatically with Multiscale Models)

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