Fetch by ID

Choosing File... Fetch by ID from the menu opens a graphical interface for fetching atomic structures, density maps, and protein sequences directly into ChimeraX from online sources. This interface includes common fetch types and uses default options. Additional fetch types and/or different options (such as to limit the number of biological assemblies obtained) can be accessed with the open command. See also: Download DICOM, Build Structure, Volume Viewer, Sequence Viewer, Web Access preferences

Clicking the desired fetch type highlights it and shows an entry field for the appropriate identifier. Hitting return (Enter) or clicking the Fetch button opens the specified data in ChimeraX. The fetch type most recently used is remembered in preferences and automatically chosen the next time Fetch by ID is shown. Close simply dismisses the dialog, whereas Help opens this page in the Help Viewer.

Ignore cached fetches indicates whether to fetch the data from the source regardless of whether it is already present in the local cache. If the data is not yet cached or the option to ignore the cache is turned on, the file will be fetched anew from the source and cached. Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory), with subdirectories PDB, EMDB, etc.

Fetch types:

• AlphaFold – from the AlphaFold Database, theoretical protein structure modeled by AlphaFold and specified by UniProt name or accession number (details...)
• EDS (2Fo-Fc) – from the PDBe Electron Density Server (EDS), (2Fo-Fc) electron density map for a PDB entry (not available for all PDB entries)
• EDS (Fo-Fc) – from the PDBe Electron Density Server (EDS), (Fo-Fc) electron density difference map for a PDB entry (not available for all PDB entries)
• EMDB – electron density map from the Electron Microscopy Data Bank (EMDB)
• EMDB & fit PDBs – electron density map from the Electron Microscopy Data Bank (EMDB) and corresponding fit PDBs (if given in the EMDB map metadata) from the Protein Data Bank
• ESMFold – from the ESM Metagenomic Atlas, theoretical protein structure modeled by ESMFold (Evolutionary Scale Modeling) and specified by MGnify identifier (details...)
• IUPAC – modeled atomic coordinates specified by IUPAC name, first translated from IUPAC to a SMILES string using the OPSIN web service provided by the Centre for Molecular Informatics at the University of Cambridge, followed by the process below for SMILES
• Model Archive – theoretical atomic structure from the ModelArchive specified by its identifier in that database; see also modelcif pae
• NMR constraints – nuclear magnetic resonance (NMR) distance constraints, available for certain entries in the Protein Data Bank and specified by PDB identifier; the corresponding atomic structure should already be open (details...)
• PDB – atomic coordinates from the Protein Data Bank specified by PDB identifier
• PDB (biounit) – from the PDBe, atomic coordinates for biological assembly or assemblies specified by PDB identifier
• PDB chemical component – from the PDB Chemical Component Dictionary (CCD), idealized structure of PDB chemical component specified by CCD ID (residue name)
• PDB-REDO (map) – diffraction data (MTZ) from PDB-REDO database specified by PDB identifier; opening MTZ files requires the Clipper bundle available from the ChimeraX Toolshed (details...)
• PDB-REDO (structure) – atomic coordinates from the PDB-REDO database specified by PDB identifier
• PubChem – from PubChem3D, modeled atomic coordinates specified by PubChem compound identifier (CID), available for most but not all entries in PubChem Compound; partial charges are assigned as the atom attribute named charge
• SMILES – modeled atomic coordinates specified by SMILES string, generated using the SMILES translator provided by the National Cancer Institute CADD group
• UniProt – from UniProt, protein sequence (along with its associated sequence features) specified by UniProt name or accession number