MSSP produces a 2D plot of a single protein descriptor for a number of structurally aligned protein chains. From a total of 150 protein descriptors available in MSSP, selected out of more than 1500 parameters stored in the STING database, it is possible to create easily readable and highly informative XY-plots, where X-axis contains the amino acid position in the multiple structural alignment, and Y-axis contains the descriptor's numerical values for each aligned structure.
Note: The MSSP is aimed to be used as tool for protein chains analysis, one chain at the time from each selected PDB file. However, a user might be able to edit PDB file and join 2 or 3 or more chains into a single chain, and in that way consider changes among multichain structures on the whole protein level. The MSSP is not yet dealing with ligand properties as those need separate calculations and we are not offering such data at the moment.
To load a 2D plot for a given parameter, just click the parameter's name in the Selection Control Panel (Figure 4).
Hovering the mouse pointer over the MSSP X-Y-plot a respective amino acid residue identification will show up. At the same time a green colored points will show up, highlighting all the other neighbour residues. To change the neighbourhood definition with respect to maximum distance of the neghbors from the central amino acid residue, right click any given Amino acid residue (2D-plot point) to open the settings menu, select the option Set Maximum Neighbour Distance and set the maximum distance value (Figure 5).
You can select a specific amino acid residue by clicking with the mouse left button the point representing that residue. If the option Select Neighbours is checked in the settings menu (Figure 6), then the points belonging to neighbours residues will also be selected.
For selecting all the residues whose displayed parameter value is less than the value of a selected parameter for a given residue r, just click the "<" button and then select the residue r. Conversely, clicking the ">" button will allow the selection of residues whose parameter value is greater than the given threshold. Selected residues can be highligted on the Jmol (3D) window by clicking Sting It. If you want to export the selected residues data to text file format, click Textual info.
Clicking a selected residue will undo the selection.
You can also select residues belonging to a specific region of the MSSP-2D plot (Figure 7). First, enable the region select mode by clicking Select AA Region.
Now if you click with the mouse left button at any point of the graph, a yellow line will mark the residues at the respective alignment position.
Then if you click at another position with the right button, the selected region will be shown as a yellow rectangle on the MSSP-2D plot,
and also the residues belonging to this region will be highlighted on the Jmol window.
Instructions on how to customize graph components (background, borders, captions, rectangles and so on) can be found at the XYgraphics module help page.