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This page is part of the DAS 1.53E specification

Volume maps extensions

Retrieve volume map data for 3D Electron microscopy structures
Version: 1.2.20070413 (April 13th, 2007)
Authors: Jose Ramon Macias, Jose-Maria Carazo, Natalia Jiménez, Joan Segura Mora
Used by DAS client: PeppeR
Reference:
Integrating electron microscopy information into existing Distributed Annotation Systems.
JR Macias, N Jimenez-Lozano, JM Carazo
J Struct Biol, 2007
[medline]
Scope: Reference servers
Command: volmap
Format: 

PREFIX/das/3DEM_Reference/volmap?query=volumeID

Description: To get a list of available volume maps for query, client may use the entry_points request.
Arguments: query (required; one): the volume map identifier. E.g.: EMD1017
Response: The response to the volmap command is the "DASVOLMAP.xml" XML-formatted document, as defined in the "dasvolmap.dtd" document type definition. This would be, in fact, the 3D-EM structural counterpart of the DASDNA.xml or DASSEQUENCE.xml documents.
Format: DASVOLMAP.xml 
<?xml version="1.0" standalone="no"?>
<!DOCTYPE DASVOLMAP SYSTEM "http://biocomp.cnb.uam.es/das/dtd/dasvolmap.dtd">
<DASVOLMAP>
 <VOLMAP id="volume_map_ID" class="volume_map" type="ccp4" version="1.0">
  <LINK href="link_to_the_volume_map_file">
    link_to_the_volume_map_file
  </LINK>
 </VOLMAP>
 <NOTE>
  NOTE: The LINK element points to the location where a 3D-EM DAS client should 
   retrive the data for the volume map (ussully through ftp)
 </NOTE>
</DASVOLMAP>
dasvolmap.dtd 
<?xml version="1.0" encoding="UTF-8"?>

<!ELEMENT DASVOLMAP (VOLMAP, NOTE*)>
<!ATTLIST DASVOLMAP version CDATA #IMPLIED>

<!ELEMENT VOLMAP (LINK)>
<!ATTLIST VOLMAP id CDATA #REQUIRED>
<!ATTLIST VOLMAP class CDATA #REQUIRED>
<!ATTLIST VOLMAP type (ccp4 | mrc) #REQUIRED>
<!ATTLIST VOLMAP version CDATA #REQUIRED>
<!ELEMENT LINK (#PCDATA)>
<!ATTLIST LINK href CDATA #REQUIRED>

<!ELEMENT NOTE (#PCDATA)>

Example: http://biocomp.cnb.uam.es:9000/das/3DEM/volmap?query=EMD1017

Detailed explanation:
Element: DASVOLMAP (required; one only). The root element of the document.
Attribute: version (optional). Indicates the version of the implementation of this DAS command. If not specified, 1.0 is assumed.
Element: VOLMAP (required; one or more). Actually, the definition of the volume map.
Attribute: id (required; one only). The identifier of the 3D-EM structure in the data base.
Attribute: class (required; one only). To indicate this structure is a 3D-EM volume map.
Attribute: type (required; one only). Volume maps can come in two file formats: CCP4 or MRC.
Attribute: version (required; one only). Version of the volume map in the data base.
Element: LINK (required; one only). Instead of the DASSEQUENCE document, the server provides just a link to the data, due to its huge size.
Attribute: href (required; one only). An URL where to retrieve the file containing the volume map.
Element: NOTE (optional). Text information in human readable format that a client may show directly top the user. In this case it is used only to remind how the volume map file can be directly retrieved from the Server.