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. Fetched files can be cached locally and reused as needed depending on the Fetch preferences and PDB preferences.

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. Next, Chimera will look for the file in any personal PDB directories designated in the PDB preferences.
  3. Next, the PDB subdirectory of the fetch download directory will be checked (unless the use of previously fetched files has been disallowed in the Fetch preferences).
  4. Finally, if not found locally, the file will be fetched from the Protein Data Bank web site (unless fetching has been disallowed 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 modeled 3D structure (SDF) from the Pub3D database via a web service provided by the CICC at Indiana University. Pub3D is described in Willighagen et al., BMC Bioinformatics 8:487 (2007). About 99% of the compounds in PubChem are available; the structure generation pipeline generally handles organic compounds, but not inorganic, metallo-, or highly unstable species such as radicals.
• 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)
• 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)
• EMDB - a numerical identifier will be used to fetch an electron density map from the Electron Microscopy Data Bank (see also keyword search)
• EMDB & fit PDBs - a numerical identifier will be used to fetch an electron density map from the Electron Microscopy Data Bank, along with any corresponding PDB entries, which may or may not be in the fit positions relative to the map (see also keyword search)
• 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)

Clicking Set download directory opens the Fetch preferences for specifying a local directory in which to save fetched files.

Close dismisses the dialog without retrieving the data. Help brings up this manual page in a browser window.

Currently keyword searching is only available for the EMDB. The reference title, reference authors, and ID number fields are searched.

Typing a word or phrase into the search field and pressing return (Enter) or clicking Search initiates a case-independent search. If multiple words are supplied, only entries with the words present as a contiguous phrase (together and in the order given) will be found. Matching entries will be listed in a separate dialog, from which they can be retrieved by choosing the line(s) of interest and clicking Fetch Map or Fetch Map and PDBs.