In version 1.2, the pixel plot consisted of a black pixel for each residue and a white pixel for each gap as shown in Figure 1.A. In SuiteMSA version 1.3, the residue pixels can be color-coded as shown in Figure 1.B. The four possible structure-data based color-schemes are as follows:

1. Transmembrane structure
2. Secondary structure
3. Rank data (red/yellow)
4. Ranked data (blue/green)

The structural information for each sequence (in FASTA format) must be provided to use this color-scheme option. Sequence names must be exactly the same between the alignment file and the structure data file. See section 2 for more details on how to prepare structural data file.

After the first pixel plot has been opened (Figure 2.A), there are two ways to access these color schemes. To change the color scheme of the existing pixel plot, click on the Change color button immediately above the pixel plot you want to change the color. This will bring up a pop-up window where you can choose the type of structural data. After the structural data file is selected, the pixel plot will be color-coded by the information provided (Figure 2.B).

To open an additional display of the same alignment with a different color scheme, click on the Add structure button. After selecting the type of structural data, a new pixel plot will be displayed color-coded by the information provided in the file (Figure 2.C).