Difference between revisions of "Database Connection"

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== Connection of Jmol to databases ==
+
= Summary =
 +
Shorthand notations (read below for details and explanation):
 +
 
 +
{| class="wikitable"
 +
|- style="text-align: center;"
 +
! RCSB PDB
 +
! RCSB Ligands
 +
! EBI PDB <br>Europe
 +
! NCI <br>(Cactus)
 +
! PubChem
 +
! CrystOD
 +
|- style="text-align: center;"
 +
| =
 +
| ==
 +
| *
 +
| $
 +
| :
 +
|
 +
|- style="text-align: center;"
 +
| =pdb/
 +
| =ligand/
 +
| =pdbe/
 +
| =nci/
 +
| =pubchem/
 +
| =cod/
 +
|}
 +
 
 +
= Connection of Jmol to databases =
 
Jmol can connect to certain databases in order to directly retrieve structures.
 
Jmol can connect to certain databases in order to directly retrieve structures.
−
This applies to the Jmol application and to the Jmol signed applet.
+
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:
 +
<pre style="margin-left:5ex;">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>
 +
</pre>
  
 
== PDB ==
 
== PDB ==
−
(The [http://www.pdb.org RCSB Protein Data Bank])
+
(The [http://www.pdb.org RCSB Protein Data Bank], also Wordlwide PDB, wwPDB)
  
 
Macromolecular structures may be retrieved from the PDB database:
 
Macromolecular structures may be retrieved from the PDB database:
 
* Using the Jmol application, top menu bar <code>File > Get PDB</code>. A dialog is displayed where you can type a 4-character PDB ID.
 
* Using the Jmol application, top menu bar <code>File > Get PDB</code>. 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: <code>load =1crn</code> for crambin.
+
* Using the script language:  
 +
** use '''an equal sign''' followed by the 4-character PDB ID (no spaces). Example: <code>load =1CRN</code> for crambin.
 +
** use '''an equal sign''' followed by <code>pdb</code>, a forward '''slash''', and the 4-character PDB ID. Example: <code>load =pdb/1CRN</code> for crambin.
  
−
Ligand structures can also be retrieved from the PDB:
+
For additional options (nucleic acid secondary structure, validation or domain annotations), see [{{ScriptingDoc}}#loadfiletypes the <code>load</code> command]
−
* Using the Jmol application, top menu bar <code>File > Get PDB</code>. You must type a = sign before the 3-character PDB ID of the ligand.  
+
 
−
* Using the script language: use two equal signs. Example: <code>load ==etb</code> for ethyl-coenzyme A.
+
Ligand structures can also be retrieved (in CIF format) from the PDB:
 +
* Using the Jmol application, top menu bar <code>File > Get PDB</code>. You must type an equal sign before the 3-character PDB ID of the ligand.  
 +
* Using the script language:  
 +
** use '''two equal signs'''. Example: <code>load ==ETB</code> for ethyl-coenzyme A.
 +
** use '''an equal sign''' followed by <code>ligand</code>, a forward '''slash''', and the 3-character ID. Example: <code>load =ligand/ETB</code>
 +
===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 <code>%FILE</code> at the position where the PDB ID should be inserted into the url.
 +
[{{ScriptingDoc}}#set_loadformat More details]
 +
 
 +
Examples:
 +
set loadFormat = "<nowiki>https://files.rcsb.org/download/%FILE.pdb</nowiki>"
 +
set loadFormat = "<nowiki>http://www.ebi.ac.uk/msd-srv/oca/oca-bin/save-pdb?id=%FILE</nowiki>"
 +
set loadLigandFormat = "<nowiki>https://files.rcsb.org/ligands/download/%FILE.cif</nowiki>"
 +
 
 +
=== PDB Europe ===
 +
[http://www.pdbe.org 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: <code>load *1CRN</code> for crambin.
 +
** use '''an equal sign''' followed by <code>pdbe</code>, a forward '''slash''', and the 4-character PDB ID (no spaces). Example: <code>load =pdbe/1CRN</code>
 +
 
 +
For additional options (nucleic acid secondary structure, validation or domain annotations), see [{{ScriptingDoc}}#loadfiletypes the <code>load</code> command]
  
 
== NCI/NIH ==
 
== NCI/NIH ==
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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...
 
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 <code>File > Get MOL</code>. A dialog is displayed where you can type the name or identifier.
 
* Using the Jmol application, top menu bar <code>File > Get MOL</code>. 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: <code>load $aspirin</code>; <code>load "$acetylsalycilic acid"</code>
+
* 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: <code>load $aspirin</code>; <code>load "$acetylsalycilic acid"</code>
 +
** use '''an equal sign''' followed by <code>nci</code>, a forward '''slash''', and the name or identifier. Example: <code>load =nci/aspirin</code>
 +
 
 +
===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 <code>%FILE</code> at the position where the name or ID should be inserted into the url.
 +
[{{ScriptingDoc}}#set_loadformat More details]
 +
 
 +
Examples:
 +
set nihResolverFormat = "<nowiki>https://cactus.nci.nih.gov/chemical/structure/%FILE</nowiki>"
 +
set smilesURLformat = "<nowiki>https://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=true</nowiki>"
 +
 
  
 
== PubChem ==
 
== PubChem ==
Line 26: Line 107:
 
Chemical structures may be retrieved from this database by name
 
Chemical structures may be retrieved from this database by name
 
* Using the Jmol application, top menu bar <code>File > Get MOL</code>. A dialog is displayed where you can type the name or identifier, prefixed with a : sign.
 
* Using the Jmol application, top menu bar <code>File > Get MOL</code>. 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: <code>load :aspirin</code>; <code>load ":acetylsalycilic acid"</code>
+
* 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 <code>pubchem</code>, a forward '''slash''', and the name or identifier.
 +
Examples:
 +
* <code>load :aspirin</code>
 +
* <code>load =pubchem/aspirin</code>
 +
* <code>load ":acetylsalycilic acid"</code>
 +
For a more explicit indication of the kind of identifier that is being provided, a tag and an extra colon are included:
 +
* <code>load :name:tylenol</code>
 +
* <code>load :cas:103-90-2</code>
 +
* <code>load :cid:1983</code>
 +
* <code>load :smiles:CC(=O)Nc1ccc(cc1)O</code>  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 <code>%FILE</code> at the position where the name or ID should be inserted into the url.
 +
 
 +
Example:
 +
<nowiki>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d</nowiki>
 +
 
 +
 
 +
== Crystallographic Open Database ==
 +
The [http://www.crystallography.net/ COD website] holds an open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers.
 +
:''(This feature was added in Jmol Version 14.3.12_2015.01.21)''
 +
 
 +
Chemical structures (in CIF format) may be retrieved from this database by numeric code:
 +
* Using the script language: use '''an equal sign''' followed by <code>cod</code>, a forward '''slash''' and the numeric code of the compound (no spaces). Example:
 +
** <code>load =cod/1000373</code>  for sodium vanadium dioxide difluoride (symmetry space group P 1 21 1)
 +
** <code>load =cod/1000373 {444 666 1}</code>  for a display of the crystalline network of the same

Revision as of 16:10, 5 December 2017

Summary

Shorthand notations (read below for details and explanation):

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

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"

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 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.

(This feature was added in Jmol Version 14.3.12_2015.01.21)

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

Contributors

AngelHerraez, Rzepa

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