To load a 2D plot for a given parameter, just click the parameter's name in the Selection Control Panel (Fig. 1).
You can select a specific amino acid residue by clicking the point representing that residue. If the option Select Neighbours is checked in the settings menu, then all points belonging to neighbours residues will also be selected. The criteria for searching neighboring residues is defined by the Cα-Cα distance. To change the search criteria, select the option Maximum Neighbour Distance and set the maximum distance value (Fig. 2).
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.
You can also select residues belonging to a specific region of the MSSP 2D Plot (Fig. 3). First, enable the region select mode by clicking Select AA Region. Then select the region by clicking and dragging.
Atfer selecting a point in the 2D Plot, the respective amino acid residue will be automatically highlighted on the Jmol (3D) window.
The XY-plot can be exported as Scalable Vector Graphics (SVG) by clicking Generate SVG Image. If you want to export the selected residues data to text file format, click the button Textual Info.