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 in a local download directory and reused as needed depending on the Fetch preferences, PDB preferences, and whether the option to Ignore any cached data is checked. See also: Rapid Access, Chimera input file types

A database and corresponding identifier (ID code) must be indicated. Multiple identifiers for the same database can be entered, separated by spaces and/or commas.

• 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 (Protein Data Bank Identifier) 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 website (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
• PDB (biounit) - a 4-character PDB ID will be used to fetch one or more PDB-format biological assembly files from the Protein Data Bank; there may be multiple assemblies for a given entry, and a specific assembly can be designated by appending “.N” to the PDB ID. For example, 1dok specifies all biological assemblies of entry 1dok, 1dok.2 specifies biological assembly 2, and 1dok.1.2 specifies biological assemblies 1 and 2. Each assembly will be opened as a separate main model number, possibly containing submodels.
• SCOP - a 7-character SCOP domain identifier will be used to fetch a PDB-format domain file from the ASTRAL database
• cellPACK - a cellPACK model identifier (see cellPACK Chimera instructions for available identifiers)
• PubChem - a PubChem compound identifier (CID) will be used to fetch a modeled 3D structure from PubChem3D (this resource includes most but not all PubChem Compound entries, e.g., only the parent forms of salts, and subject to limits on compound size, flexibility, and constituent atom types)
• 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 Protein Data Bank in Europe (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 Protein Data Bank in Europe (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 (or Chinese mirror site, for .cn hosts)
• EMDB & fit PDBs - a numerical identifier will be used to fetch an electron density map from the Electron Microscopy Data Bank (or Chinese mirror site, for .cn hosts), along with any corresponding Protein Data Bank entries, which may or may not be in the fit positions relative to the map. PDB entries only available as mmCIF will be fetched in that format instead of in PDB format.
• 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 - a 4-character PDB ID will be used to fetch a PDB-format file from the Virus Particle Explorer database of icosahedral virus capsid structures (the capsid will be constructed automatically with Multiscale Models)
• UniProt - a UniProt accession code or identifier will be used to fetch a protein sequence and its annotations and show them in Multalign Viewer (much as described for PDB/UniProt Info, except independent of structure). This type of fetch is not saved locally even if a download directory has been specified. UniProt's ID mapping service can be used to obtain UniProt identifiers from other sequence database identifiers.

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.