Database Connection - Revision history

AngelHerraez: change of American Mineralogist Crystal Structure Database URL and hence in Jmol retrieval

2025-11-16T17:50:28Z

change of American Mineralogist Crystal Structure Database URL and hence in Jmol retrieval

2025-08-20T17:59:12Z

updates to remove mention of Java applet

2025-08-20T17:40:44Z

Crystallographic Open Database - lost access

2023-08-19T09:52:02Z

adding American Mineralogist Crystal Structure Database

2021-11-25T14:48:52Z

new formats from PDB

2021-11-22T16:02:51Z

PubChem retrieve by CAS

2019-04-27T22:30:41Z

adding doc. on access to the Materials Project db

2018-06-10T19:25:06Z

‎Connection of Jmol to resources by specifying a DOI

2018-06-10T06:58:51Z

‎Connection of Jmol to resources by specifying a DOI

2018-06-09T16:48:02Z

‎Connection of Jmol to resources with DOI

@@ Line 141: / Line 141: @@
 == American Mineralogist Crystal Structure Database ==
-The [http://rruff.geo.arizona.edu/AMS/amcsd.php AMCSD website] (hosted at the University of Arizona, USA) includes every structure published in the American Mineralogist, The Canadian Mineralogist, European Journal of Mineralogy and Physics and Chemistry of Minerals, as well as selected datasets from other journals.
+The [https://www.rruff.net/amcsd/ AMCSD website] (formerly hosted at the University of Arizona, USA, now separate) includes every structure published in the American Mineralogist, The Canadian Mineralogist, European Journal of Mineralogy and Physics and Chemistry of Minerals, as well as selected datasets from other journals.
 Chemical structures (in CIF format) may be retrieved from this database by name, by 5-digit ID or by 7-digit ID. See
@@ Line 147: / Line 147: @@
 Note: calling by structure name will retrieve a multi-model file with all the crystal structures that match the search.
 == The Materials Project ==

@@ Line 30: / Line 30: @@
 | =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.
+This applies to the Jmol application and also to the JSmol object in web pages.
 == PDB ==
-(The [http://www.pdb.org RCSB Protein Data Bank], also Wordlwide PDB, wwPDB)
+(The [http://www.pdb.org RCSB Protein Data Bank] located at USA)
 Macromolecular structures may be retrieved from the PDB database:
@@ Line 62: / Line 54: @@
 ** 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).

@@ Line 136: / Line 136: @@
   <nowiki>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d</nowiki>
-== Crystallographic Open Database ==
+== Crystallography 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.
@@ Line 143: / Line 146: @@
 ** <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
 == American Mineralogist Crystal Structure Database ==

@@ Line 10: / Line 10: @@
 ! PubChem
 ! CrystOD
 ! Materials<br>Project
 |- style="text-align: center;"
@@ Line 26: / Line 27: @@
 | =pubchem/
 | =cod/
 | =mp/
 |}
@@ Line 142: / Line 144: @@
 ** <code>load =cod/1000373 {444 666 1}</code>  for a display of the crystalline network of the same
 == The Materials Project ==

@@ Line 48: / Line 48: @@
 * 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.
+** use '''an equal sign''' followed by the 4-character PDB ID (no spaces). Example: <code>load =1CRN</code>. This will retrieve the file in <code>pdb</code> format.
 ** 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.
 For additional options (nucleic acid secondary structure, validation or domain annotations), see [{{ScriptingDoc}}#loadfiletypes the <code>load</code> command]

@@ Line 117: / Line 117: @@
 * <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 :cid:1983</code>
 * <code>load :smiles:CC(=O)Nc1ccc(cc1)O</code>  Here the :smiles: tag is required
@@ Line 131: / Line 131: @@
 Example:
   <nowiki>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d</nowiki>
 == Crystallographic Open Database ==

@@ Line 144: / Line 144: @@
 Jmol can retrieve a model from a resource that complies with this:
 * the file to be loaded has a registered [[:en:Digital_object_identifier|DOI]]
-* the DOI metadata defining the path to the resource has a METS or [http://www.openarchives.org/ore/1.0/toc ORE] resource map. Y
+* the DOI metadata defining the path to the resource has a METS or [http://www.openarchives.org/ore/1.0/toc ORE] resource map.
 ** You can find out if such a resource map exists by invoking e.g. https://data.datacite.org/application/vnd.datacite.datacite+xml/10.14469/hpc/4310 where the DOI is appended. The XML metadata file as downloaded should have a string e.g. <code> <relatedIdentifier relatedIdentifierType="URL" relationType="HasMetadata" relatedMetadataScheme="ORE" schemeURI="http://www.openarchives.org/ore/">https://data.hpc.imperial.ac.uk/resolve/?ore=4310</relatedIdentifier></code>

← Older revision		Revision as of 16:48, 9 June 2018
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−	= Connection of Jmol to resources ~~with~~ DOI =	+	= Connection of Jmol to resources by specifying a DOI =

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