Documentation DAS structure service

Retreive 3D coordinates

Version: May 11th, 2006

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 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>

(optional;) 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: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.

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.

• 1a4a structure

The XML schemes proposed on this site are also part of the eFamily XML scheme at http://www.sanger.ac.uk/xml/efamily/documentation/eFamily.html.

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