Database Connection

Connection of Jmol to databases

Jmol can connect to certain databases in order to directly retrieve structures. This applies to the Jmol application and to the Jmol signed applet. (The unsigned applet is not allowed connection to external servers and so does not support this method.)

PDB

(The RCSB Protein Data Bank)

Macromolecular structures may be retrieved from the PDB database:

• Using the Jmol application, top menu bar File > Get PDB. A dialog is displayed where you can type a 4-character PDB ID.
• Using the script language: use an equal sign followed by the 4-character PDB ID (no spaces). Example: load =1CRN for crambin.

Ligand structures can also be retrieved (in CIF format) from the PDB:

• Using the Jmol application, top menu bar File > Get PDB. You must type a = sign before the 3-character PDB ID of the ligand.
• Using the script language: use two equal signs. Example: load ==ETB for ethyl-coenzyme A.

Database location

By default, Jmol will connect to the PDB server, at http://www.rcsb.org/pdb/files/ for macromolecules and at http://www.rcsb.org/pdb/files/ligand/ for ligands. To force the use of another server, you can do:

set loadFormat = "  "
set loadLigandFormat = "  "

and put between the quotes the url in the proper request format; use %FILE at the position where the PDB ID should be inserted into the url. More details

Examples:

set loadFormat = "http://www.rcsb.org/pdb/files/%FILE.pdb.gz"
set loadFormat = "http://www.ebi.ac.uk/msd-srv/oca/oca-bin/save-pdb?id=%FILE"
set loadLigandFormat = "http://www.rcsb.org/pdb/files/ligand/%FILE.cif"

NCI/NIH

National Cancer Institute, CADD Group's Chemoinformatics Tools, Chemical Identifier Resolver (CACTUS server).

Chemical structures may be retrieved from this database by using a common name, a IUPAC name, a SMILES, an InChI, an InChIKey, a Chemical Abstracts registry number...

Note: the SMILES will be converted to a 3D model in the server.

• Using the Jmol application, top menu bar File > Get MOL. A dialog is displayed where you can type the name or identifier.
• Using the script language: use a dollar sign followed by the name or identifier (no spaces). If the name contains spaces, enclose between quotes. Examples: load $aspirin; load "$acetylsalycilic acid"

Database location

By default, Jmol will connect to the CACTUS server at http://cactus.nci.nih.gov/chemical/structure To force the use of another server, you can do:

set nihResolverFormat = "  "
set smilesURLformat = "  "

and put between the quotes the url in the proper request format; use %FILE at the position where the name or ID should be inserted into the url. More details

Examples:

set nihResolverFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE"
set smilesURLformat = "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True"

PubChem

National Center for Biotechnology Information, PubChem.

Chemical structures may be retrieved from this database by name

• Using the Jmol application, top menu bar File > Get MOL. A dialog is displayed where you can type the name or identifier, prefixed with a : sign.
• Using the script language: use a colon sign followed by the name or identifier (no spaces). If the name contains spaces, enclose between quotes. Examples:
  • load :aspirin
  • load ":acetylsalycilic acid"
• For a more explicit indication of the kind of identifier that is being provided, a tag and an extra colon are included:
  • load :name:tylenol
  • load :cas:103-90-2
  • load :cid:1983
  • load :smiles:CC(=O)Nc1ccc(cc1)O // the :smiles: tag is required

Contributors

AngelHerraez, Rzepa