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Ligand Explorer

A viewer that visualizes the interactions of bound ligands in protein and nucleic acids structures. Ligand Explorer has options to turn on the display of interactions including hydrogen bonds, hydrophobic contacts, water mediated hydrogen bonds, and metal interactions.

 

How do I launch Ligand Explorer?

A link to Ligand Explorer is available in the Ligand Chemical Component widget on the structure summary page.

Launching Ligand Explorer

Read the guide about launching Java Web Start applications.

 

How do I rotate or move the Structures?

To quickly get information on structural details you may mouse over structural features in the molecular viewer window as well as the sequence viewer at the top. Information regarding structural details such as residue number and element type is displayed in the status bar at the bottom of the viewer.

Basic Commands
Rotate Click (windows: left click) in the 3D window and drag the mouse up, down or left and right.
Zoom Hold down the shift key while dragging the mouse up and down.
Translate Hold down the control key while dragging the mouse on the 3D graphics window.

 

How are the Structures rendered?

Feature Style Color
Protein Chain Wireframe Rainbow spectrum from N-terminus (blue) to C-terminus (red)
Nucleic Acid Chain Wireframe Rainbow spectrum from 5' end (blue) to 3' end (red)
Ligands and Modified Residues Ball-and-Stick Atoms are colored by element:

carbon - green
hydrogen - white
oxygen - red
nitrogen - blue
sulfur - yellow
phosphorus - orange

A full list of element colors can be found at: http://jmol.sourceforge.net/jscolors

 

How do I display Interactions with the Ligand?

First, select a ligand from the left hand menu. If you launched Ligand Explorer from the Ligand Chemical Component widget, a ligand is already selected. Second, click the check boxes next to the list of interactions to turn on the interactions.

Ligand Interactions

Interacting residues and the distance of the interactions are automatically displayed, as shown in the example below. Interacting residues are also highlighted with grey boxes in the sequence display.

Ligand Interactions

 

What types of Interactions are available?

Each interaction type has a default distance threshold, i.e. 3.3 A for hydrogen bonds. You can change these values by typing in a new value and hitting the Enter key.

 

How do I save a High-Resolution Image?

Follow the tutorial (click here) for saving high-resolution images.

 

How can I view other Structures?

You can load another structure directly using the file menu using one of three options:

  1. Load a structure using the PDB ID

    Use the File -> Open PDB ID option to load a new structure by the 4-letter PDB ID (example 1STP).

  2. Load a structure from a file

    Use the File -> Open File option to load a structure in the PDB (*.pdb) and PDBML/XML (*.xml) file format (Description of file formats: http://www.pdb.org/pdb/static.do?p=file_formats/index.jsp).

  3. Load a structure from a URL

    Use the File -> Open ULR option to load a structure in the PDB (*.pdb) and PDBML/XML (*.xml) file format (Description of file formats: http://www.pdb.org/pdb/static.do?p=file_formats/index.jsp).