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This page is part of the DAS 1.53E specification

Documentation DAS structure service

Retrieve 3D coordinates


Version: May 11th, 2006
Authors: Andreas Prlic, Rob Finn, Thomas Down, Tim Hubbard
Used by DAS client: SPICE
References

Reference Please cite:

Integrating sequence and structural biology with DAS
Andreas Prlic, Thomas A Down, Eugene Kulesha, Robert D Finn, Andreas Kahari, Tim JP Hubbard
BMC Bioinformatics 2007, 8:333 (12 September 2007)
[abstract] [pdf] [pubmed] [related articles]

Scope: Reference servers.
Command: structure
Format: 

PREFIX/das/structure?query=structureID[&chain=chainID&model=modelNumb&range=RANGE]

Description: This query returns coordinates for 3D objects.
Arguments:
query (required; one) the id of the object to return. e.g. PDB-id , SCOP domain id, etc.
chain (optional; one or more) the chainID to return. if the query structureID consists of several chains only selected chains are returned. if it is omitted all available chains are returned.
model (optional; one or more) the modelNum to return. if the query structureID has been resolved using NMR, several alternate models are available. using this argument it is possible to request only individual models. If it is omitted, all available models are returned.
range (optional;) this can be provided to request a particular range of a PDB structure. The RANGE is defined by 
start:stop
where both start and stop are defined as consisting of: 
pdbresnum_insertionCode.chainId
where the pdbresnum is mandator and insertionCode and chainId are optional. The . and _characters are used as separators. examples for valid ranges: 
?query=5pti&range=15:30
?query=1h4w&range=200.A:221_A.A

Response:


The response to the structure command is the "DASSTRUCTURE" XML-formatted document:
Format: 
<?xml version="1.0" standalone="no"?>
<dasstructure xmlns="http://www.efamily.org.uk/xml/das/2004/06/17/dasstructure.xsd" xmlns:data="http://www.efamily.org.uk/xml/data/2004/06/17/dataTypes.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.efamily.org.uk/xml/das/2004/06/17/dasstructure.xsd" >

	<object dbAccessionId="someid" objectVersion="version" type="objectType" dbSource="someSouce" dbVersion="version" dbCoordSys="coords"  >			
	</object>

	<objectDetail dbSource="someSouce" property="property">
			some details about the object. e.g. description, etc. 
	</objectDetail> 

	<chain id="chainID" model="modelNr" SwissprotId="accessionCode">	
		<group name="groupName" type="groupType" groupID="groupID" insertCode="iCode">
			<atom x="xCoord" y="yCoord" z="zCoord" atomName="atomname" atomID="atomID" occupancy="occupancy" tempFactor="tempFactor" altLoc="altLoc"/>
		</group>

	</chain>

	<connect type="connectionType" atomSerial="atomID" >
		<atomID atomID="atomID"/>
	</connect>
	
</dasstructure>
Element:<object> (required) A description of the structure object.
Attributes:
attribute:objectVersion (required) version of Object. e.g. MD5 checksum for protein sequences.
attribute:type (optional) a type for this object.e.g. DNA, PROTEIN, STRUCTURE, etc.
attributeGroup:dbRef This attribute group is used for referring to a database.
attribute:dbSource (required). The name of the database.
attribute:dbVersion (required). The version of the database.
attribute:dbCoordSys (optional). The co-ordinate system of used by the database. This is not always the same as the database. For example, Pfam uses UniProt as an underlying co-ordinate system.
attribute:dbAccessionId (required). The database entry accession id. For example, SCOP have sunid, Pfam accessions(PF01020).
Element:<objectDetail> (optional; zero or more) details about the object
attributeGroup:detail The following attributes are bundled together to form a group of attributes that are capable of describing additional information about a particular node.
attribute:dbSource(required). The database where the information about this source orginates.
attribute:property(required). A description of the CDATA. For example, if you wanted to give an alternative id for a database, e.g. a UniProt ID , then the <someDetail dbSource="UniProt" property="id">P50225</someDetail>
Element:<chain> (zero or more) groups everything that belongs to a chain.
Attributes:
attribute:id (required) is the Identifier for this chain, e.g. "A","B"
attribute:model (optional) if the structure is an NMR structure, this gives the model number of the current chain.
attribute:SwissProtId (optional) SwissProt accession code that is related to this chain
Element:<group> (optional;) a group of atoms. e.g. representing an amino acid or a hetero molecule.
attribute:type (required) the type of the group. e.g. amino, nucleotide, hetatom.
attribute:name (required) the name of the group. e.g. ALA
attribute:groupID (required) the PDB code of the amino acid. e.g. 25,26,27A
attribute:insertCode (optional) insertion code for amino acid. e.g 86A, 86B
Element:<atom> (required; one or more) a single atom.
Attributes:
attribute:x, attribute:y, attribute:z required) the coordinates of the atom.
attribute:atomName (required) The PDB file notation is used. e.g. " N "
attribute:atomID (required) PDB number of atom. e.g. 148,149,150A,151B
attribute:occupancy (optional) Occupancy.
attribute:tempFactor (optional) Temperature factor.
attribute:altLoc (optional) the PDB alternate location field.
Element:<connect> (optional) connectivity between atoms. for amino acids the connectivity is not needed, but for HET it is mandatory, otherwise a viewer would not know how to display them.
attribute:type the type of bond
attribute:atomSerial serial number of the atom the connect information refers to .
Element:<atomID> an atom that is connected to the one specified by this connection.
attribute:atomID serial number of the atoms.
Example Responses

The SPICE DAS client for protein structures can be accessed at:
http://www.efamily.org.uk/software/dasclients/spice/