This DokuWiki plugin has several utilities accessing RCSB Protein Data Base (PDB) and NCBI Structure database to show an entry and an image.

{{pdb>[Command]:[PDB ID]}}

This plugin caches two kinds of files as media files.

1. Protein images from RCSB server in /data/media/rcsb_image/ directory
2. Structure XML summary from NCBI database in /data/media/ncbi_esummary/ directory

You can place a cached image file in the same way of that in a media file. (Find the image in rcsb_image namespace)

<float left200>

{{pdb>small:1WLA}}

</float> <float left>

<float left200>

{{pdb>medium:1WLA}}

</float> <float left>

{{pdb>large:1WLA}}

<float left200>

{{pdb>link:1WLA}}

</float> <float left> 1WLA </float>

<float left200>

{{pdb>short:1WLA}}

</float> <float left>

<float left200>

{{pdb>long:1WLA}}

</float> <float left>

<float left200>

{{pdb>searchbox}}

</float> <float left>

This command converts from PDB ID into StructureID of NCBI.

<float left200>

{{pdb>structureID:1WLA}}

</float> <float left> StructureID:57663 </float>

Combination of an image from PDB ID and a short description from NCBI.

{{pdb>fullSmall:1WLA}}

This command displays a raw data of ESummary XML data from NCBI Structure DB. The 'short' and 'long' descriptions are extracted from this file. The XML files are in /data/media/ncbi_esummary. <float left200>

{{pdb>summaryXML:1WLA}}

</float> <float left400>

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20041029//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20041029/esummary-v1.dtd">
<eSummaryResult>
<DocSum>
	<Id>57663</Id>
	<Item Name="PdbAcc" Type="String">1WLA</Item>
	<Item Name="PdbDescr" Type="String">Myoglobin (horse Heart) Recombinant Wild-type</Item>
	<Item Name="EC" Type="String"></Item>
	<Item Name="Resolution" Type="String">1.7</Item>
	<Item Name="ExpMethod" Type="String">X-Ray Diffraction</Item>
	<Item Name="PdbClass" Type="String">Oxygen Transport</Item>
	<Item Name="PdbDepositDate" Type="String">1997/09/24 00:00</Item>
	<Item Name="MMDBEntryDate" Type="String">2007/10/11 00:00</Item>
	<Item Name="OrganismList" Type="List">
		<Item Name="string" Type="String">Equus caballus</Item>
	</Item>
	<Item Name="LigCode" Type="String">HEM|SO4</Item>
	<Item Name="LigCount" Type="String">2</Item>
	<Item Name="ModProteinResCount" Type="String">0</Item>
	<Item Name="ModDNAResCount" Type="String">0</Item>
	<Item Name="ModRNAResCount" Type="String">0</Item>
	<Item Name="ProteinChainCount" Type="String"></Item>
	<Item Name="DNAChainCount" Type="String"></Item>
	<Item Name="RNAChainCount" Type="String"></Item>
</DocSum>

</eSummaryResult>

• 2016.10.24
  • URLs are changed to https according to changes in Web API of NCBI database
• 2008.3.22
  • Some functions were parted into bio plugin and cache plugin
• 2008.3.16
  • Vulnerability (XSS) was fixed.
• 2008.3.7
  • Bug fix of incorrect permission of cache files

<float icon(compass)>

• SearchNCBI plugin
• SearchDDBJ plugin
• SearchEMBL plugin
• PDB plugin

</float> <clear/>