Database Connection

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Revision as of 16:02, 22 November 2021 by AngelHerraez (talk | contribs) (PubChem retrieve by CAS)
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Summary

Shorthand notations (read below for details and explanation):

RCSB PDB RCSB Ligands EBI PDB
Europe 		NCI
(Cactus) 		PubChem CrystOD Materials
Project
= == * $ :
=pdb/ =ligand/ =pdbe/ =nci/ =pubchem/ =cod/ =mp/

Connection of Jmol to databases

Jmol can connect to certain databases in order to directly retrieve structures. This applies to the Jmol application, to the JSmol HTML5 object and to the Jmol signed Java applet. (The unsigned applet is not allowed connection to external servers and so does not support this method.)

Note: After some changes (2016) in the way some databases are allowing access, old versions of Jmol will fail to retrieve the structures. Updating your Jmol will fix this problem. Example of this failure:
ERROR in script: unrecognized file format for file
http://cactus.nci.nih.gov/chemical/structure/tylenol/file?format=sdf&get3d=True
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>301 Moved Permanently</title>

PDB

(The RCSB Protein Data Bank, also Wordlwide PDB, wwPDB)

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.
    • use an equal sign followed by pdb, a forward slash, and the 4-character PDB ID. Example: load =pdb/1CRN for crambin.

For additional options (nucleic acid secondary structure, validation or domain annotations), see the load command

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 an equal 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.
    • use an equal sign followed by ligand, a forward slash, and the 3-character ID. Example: load =ligand/ETB

Database location

By default Jmol will connect to the PDB server at https://files.rcsb.org/download/ for macromolecules (when using the '=id' option) and at https://files.rcsb.org/ligands/download/ for ligands (when using the '==id' option). 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 = "https://files.rcsb.org/download/%FILE.pdb"
set loadFormat = "http://www.ebi.ac.uk/msd-srv/oca/oca-bin/save-pdb?id=%FILE"
set loadLigandFormat = "https://files.rcsb.org/ligands/download/%FILE.cif"

PDB Europe

EMBL-EBI's Protein Data Bank in Europe (PDBe) keeps a mirror of the PDB data.

To retrieve models from them, in mmCIF format:

  • Using the script language:
    • use an asterisk sign followed by the 4-character PDB ID (no spaces). Example: load *1CRN for crambin.
    • use an equal sign followed by pdbe, a forward slash, and the 4-character PDB ID (no spaces). Example: load =pdbe/1CRN

For additional options (nucleic acid secondary structure, validation or domain annotations), see the load command

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 reasonable 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"
    • use an equal sign followed by nci, a forward slash, and the name or identifier. Example: load =nci/aspirin

Database location

By default, Jmol will connect to the CACTUS server at https://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 = "https://cactus.nci.nih.gov/chemical/structure/%FILE"
set smilesURLformat = "https://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.
    • use an equal sign followed by pubchem, a forward slash, and the name or identifier.

Examples:

  • load :aspirin
  • load =pubchem/aspirin
  • load ":acetylsalycilic acid"
  • load ":103-90-2" (a number ID in Chemical Abstracts Service)

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 :cid:1983
  • load :smiles:CC(=O)Nc1ccc(cc1)O Here the :smiles: tag is required

Database location

By default, Jmol will connect to the PubChem server at https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/ To force the use of another server, you can do: 

set pubChemFormat = "  "

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.

Example: 

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d

Crystallographic Open Database

The COD website holds an open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers.

Chemical structures (in CIF format) may be retrieved from this database by numeric code:

  • Using the script language: use an equal sign followed by cod, a forward slash and the numeric code of the compound (no spaces). Example:
    • load =cod/1000373 for sodium vanadium dioxide difluoride (symmetry space group P 1 21 1)
    • load =cod/1000373 {444 666 1} for a display of the crystalline network of the same


The Materials Project

The Materials Project provides open web-based access to computed information on known and predicted materials.


Connection of Jmol to resources by specifying a DOI

Jmol can retrieve a model from a resource that complies with this:

If the resource map exists, a mechanism may be implemented to retrieve the model from the DOI value into JSmol. There is an example here, including links of the form:

<a href="javascript:handle_jmol('10.14469/hpc/4310',%20';frame 1;spin 3;')">Load using a DOI</a>

where 10.14469/hpc/4310 is the DOI. This only points to the DOI landing page and requires the deposition metadata which points to the resource map and which in turn defines the path to the required file from the landing page. In this instance, the request retrieves by default a Gaussian log file, but the default can be reconfigured in the resolve-doi.js file.

The function handle_jmol() is processed in a custom JavaScript called resolve-doi.js (included in that example page). This works at least for a DSpace repository (which uses METS resource maps) and the Imperial repository (which uses ORE).

Note: If anyone knows of molecular files in other METS or ORE compliant data repositories, please share with Henry Rzepa

Contributors

AngelHerraez, Rzepa

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