The iPfam structure page offers visualization via JSmol of all structures that are available in the database. For each structure, the protein chain or chains are rendered as white ribbon cartoons, depicting the secondary structure elements.
The positions of Pfam domains are indicated on the structure by colouring the ribbon, with each Pfam domain in the structure assigned a unique colour. Ligands, if present, are shown as a ball-and-stick representation and coloured according to the CPK scheme. Use of the JSmol plugin is limited to browsers that support HTML5 and Canvas.
Visualizing a domain of interest in a structure is complicated by factors such as the size, the number of the domains or the presence of multiple copies of the same domain.
To make identifying each domain in a structure easier, you can switch to ‘Family’ annotations using the radio button found in the annotation selection block. If you place your mouse cursor over the domain of interest in the table, it causes the corresponding domain in the structure to be highlighted.
Similar highlighting is also available for ligands, but rather than changing the colour, the ball and stick representation of the ligand is enlarged. By clicking the family or ligand name (or accession) you will be taken to the corresponding page for that item.
To view the details of an interaction, you first need to choose the desired interaction annotation (DDI or DLI) using the radio buttons in the annotation selection block.
From here you can click the “>” symbol in the table of annotations. This click triggers the following set of events:
- Reveals the list of bonds (hidden by a subsequent click of the “v” symbol)
- Renders the bonds on the structure
Activates the tool bar underneath the JSmol pane. This toolbar contains three buttons that control how much structure information is displayed. The ‘’ button shows the entire structure.
To provide a less obscured investigation of each domain interaction, you can hide the parts of the structure that do not belong to the interacting domains by clicking on the ‘’ buttons. The ‘’ button restricts the display still further, so that just the interacting residues are visible.
In all three views, the nested table showing the list of bonds can be used to modulate the display of each bond, by clicking on the checkboxes. All van der Waals bonds can be toggled off using the button in the table header (labelled ‘ VDW’), leaving just the higher order bonds.
You can also click the interaction (name in ‘’ column) to jump to the 2D representation of this interaction. (see Interactions help)