2. Convert your sequence alignment to a property file

• If your input is a plain file containing your scalar data to map, such as heteronuclear NOE or chemical shift differences, ensure the first column in your file contains residue numbers and the second column contains the values to map, then click the Browse button to retrieve this file and select "Plain list of scores"

• If your input is a file saved from a BLAST session in step 1, or if your input is an alignment file in MSF or CLUSTAL format, click the Browse button to retrieve this file and select "BLAST, MSF or CLUSTAL file". 


• If your input is a sequence alignment saved from a previous ProtSkin query, click the Browse button to retrieve this file and select "Sequence alignment (from a previous query)". 

By default, redundant sequences in the alignment will not be considered. If you do not want this, uncheck the "Discard" option. In any case, insertions in the query sequence will be discarded and lowercase letters will automatically be converted to uppercase.

The conservation property calculated for each residue in the alignment can be :    
    - the percentage of identity to the query sequence, or to the consensus sequence, or    
    - the average similarity score to the query sequence, or to the consensus sequence.
Similarity scores are calculated using the traditional BLOSUM62 Block Substitution Matrix.
Select the appropriate options.

In the "PDB file" section, click the Browse button to retrieve the PDB file you will use for the structure of your protein. Select your favorite color. If you want to highlight the lower values instead of the higher ones, check the "Invert colors" option (only colors, not values, will be affected).

In the end, click the Process button to convert your data to a property file.