Fetch by ID
Structures 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.
A database and corresponding identifier (ID code) must be indicated:
Clicking Fetch retrieves the indicated data
and dismisses the dialog (although there is a checkbox option to
Keep dialog up after Fetch).
Clicking Web Page opens the home page of the chosen database
if no ID code has been entered, or the specific page for the entry if
a valid ID code has been entered.
- 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:
- 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.
- If the file is not found locally, Chimera will try to retrieve it
Protein Data Bank web site
(by default; this can be turned off in the
- 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
- EDS - a 4-character
will be used to fetch an electron density map from the
Density Server (not all PDB entries have maps available;
Volume Viewer will be used to show the map)
- VIPERdb - an identifier in the
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
Close dismisses the dialog without retrieving the data.
Help brings up this manual page in a browser window.
UCSF Computer Graphics Laboratory / June 2006