JS MSSP Interface

A JSMSSP running application is composed of four main components:

  1. A sequence frame showing the sequence alignment that obeys the generated structural alignment (Fig. 1A).
  2. A 2D Plot of a selected protein descriptor considering the structural alignment (Fig. 1B).
  3. A visualization panel displaying the structural alignment (Fig. 2A). The structural alignment renderization is performed by the previously chosen visualization program (PV or JSmol).
  4. A control panel for the selection protein descriptors (Fig. 2B).

Loading a 2D Plot

To load a 2D Plot for a given protein descriptor, just click the descriptor's name in the Descriptor Selection Control Panel (Fig. 2B). The available descriptors are organized into six groups: Structural, Geometric, Contacts, Physical-Chemical, Conservation and Others.

Residues Selection

You can select a specific amino acid residue by clicking the point representing that residue in the 2D Plot. Residues can be also selected by dragging the mouse over the aligned sequences within the sequence frame.

Clicking a selected residue will undo the selection. By clicking the button Clear the Viewport, all selected points that belong to the current viewport (i.e. that are visible) will be deselected.

Atfer selecting a point in the 2D Plot, the respective amino acid residue will be automatically highlighted on the Protein Viewer display. Deselecting points will also affect the rendered structural alignment.

In order to select all the residues whose parameter value is less than the value for a given residue r, just click the < button and then select the point representing that residue r. Conversely, clicking the > button will allow the selection of residues whose parameter value is greater than the given threshold.

If the Neighbors mode is on, clicking a point in the 2D Plot will select all the points corresponding to neighboring residues. The criteria for searching neighboring residues is defined by the Cα-Cα distance. To change the search criteria, select the option Set Max. Neighbors Distance located on the top right corner of the 2D Plot panel (Fig. 1B).

You can also select residues belonging to a specific region of the 2D Plot. First, zoom in on that specific region by clicking and dragging. Then click the button Select All Points in the Viewport.

Exporting Data

The XY-plot can be exported as Scalable Vector Graphics (SVG) by clicking Export Image. If you want to export the selected residues data to text file format, click the button Textual info.

Tutorial Video

Selecting a specific region at MSSP 2D Plot