Data Field Explanations

Accession Id:	PMDB Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the metabolite's name
Common Name:	Common name of metabolite
Synonyms:	Common synonyms for the metabolite gathered from various sources
Chemical IUPAC Name:	IUPAC or standard chemical name for the metabolite
Chemical Formula:	Chemical formula describing atomic or elemental composition
Description:	Description of the metabolite describing its metabolic role, general function, and other useful data
Molecular Weight:	Molecular weight in g/mol, determined from molecular formula.
Structure:	Image of the metabolite structure
CAS Registry Number:	Chemical Abstract Service identification number
Smiles:	Simplified Molecular Input Line Entry System, a line notation (a typographical method using printable characters) for entering and representing molecules (Canonical)-SMILES string corresponding to the non-chiral metabolite structure (Isomeric)-SMILES string corresponding to the isomeric (chiral) metabolite structure
KEGG Compound ID:	Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)
PubChem Compound ID:	NCBI's PubChem database compound identification number (if molecule is in PubChem)
PubChem Substance ID(s):	NCBI's PubChem database substance identification number (if molecule is in PubChem)
ChEBI ID:	EBI's Chemicals of Biological Interest identification number (if molecule is in CHEBI)
File formats:	MOL File -Text version of metabolite structure in Mol file format SDF File -Text version of metabolite structure in SDF file format PDB File -Text version of metabolite structure in PDB file format

Search the PMDB Database

The basic search form in plant metabolome database offers three different search options by Enter the following.

Common name
Pmdb id
synonyms

The search will show you all the relavant records in the database with Name,Pmdb id,Formula. By clicking the first accession number (PMDBID) you will get the Detail view of compound.

Navigation

If there are more than 10 results meeting the search criteria they will be displayed on multiple pages. The user can navigate through the display list using the arrows at the bottom of each page or by clicking individual page numbers:

JMol-Java Molecular Viewer

Software Requirements

Internet Explorer 6.0 on Windows XP
Safari on Mac OS 10.3.3
Mozilla 1.6 on Linux (Redhat 8.0)

Hardware Requirements

400 MHz + 128 Mb ram

More JMOl help

Jmol offers a large number of options for selecting portions of a structure and rendering them in different ways (for example showing a space filled representation of a ligand and a ribbon diagram of the main protein chain). This can be accomplished by right clicking on the applet, and by choosing "Select", "Render", and "Color" from the cascading menu. Other convenient features include the ability to continuously spin the structure, or to visualize the crystal axes or unit cell boundaries.

The left-hand mouse button can be used to rotate the molecule and the mouse scroll wheel to zoom in or out. Right clicking on the applet will display a pop-up menu through which various options to change the representation of the image can be accessed.

Java-enabling Your Browser

Jmol an open source molecule viewer that requires the installation of Java Runtime Environment.

Installing Java Runtime Environment

If it is not already installed on your system, when you try to access molecular viewers that require Java Runtime Environment you will see a message in the browser's window prompting you download the .exe installer file that contains the installer for JRE and the Java plug-in.

Follow the instructions:

Once downloaded, depending on your computer's configuration and browser, you may need to double click on the installer to start the installation. You may also need to close and restart the browser or just click again on the message window.