pdbLocation = noah_structure_path + searchPDB #This is the location of the pdb file
    natural_sequences =  af.get_natural_sequences_noah(file) #Gets a list with the natural sequences 
    cut_natural_sequences = af.get_cut_natural_sequences(identity, natural_sequences)
    print "Length of Cut Natural Sequences: " + str(len(cut_natural_sequences[0]))
    ancestor = cut_natural_sequences[0] #Gets the "ancestral sequence"
    ancestor_length = len(ancestor) #Grab the length of the ancestral sequence
    print "Ancestor Length: " + str(len(natural_sequences[0]))

    #list of files that contain L vs RSA data
    data = []

    #list of sequences with missing RSA values
    bad_list = []

    #Get all the RSA values using DSSP
    seq_data = af.get_noah_RSA_values(pdb_id, chain_id)	
    RSA = seq_data[1] #Get the RSA values
    RSA_dict = seq_data[2] #Get the dict mapping positions to RSA
    new_RSA = af.get_cut_RSA_values(pdb_id, RSA, RSA_dict)

    index = 0
    #Arrays full of the designed and natural sequences
    natural_data_arr = cut_natural_sequences
    designed_data_arr = af.get_cut_designed_sequences(designed_file)
 
    fpW_natural = open("results_array_natural_" + pdb_id + "_" + chain_id + ".csv","w")
    fpW_designed = open("results_array_" + pdb_id + "_" + chain_id + "_" + "soft" + ".csv","w")

    #write the RSA values:
    fpW_natural.write(af.dump_csv_line(new_RSA))
    fpW_designed.write(af.dump_csv_line(new_RSA))
            gap_locations.append(counter) #This is an array that tracks which residues have gaps
        counter = counter + 1

    #This section takes out the ancestral gaps from all the aligned sequences and then writes the files
    #to the results_PDB_ID_CHAIN_ID.csv 
    natural_pdb_file_title = "results_natural_" + pdb_id + "_" + chain_id + ".csv"
    natural_out_sequences = open(natural_pdb_file_title,"w") 

    #list of files that contain L vs RSA data
    data = []

    #list of sequences with missing RSA values
    bad_list = []

    #Get all the RSA values using DSSP
    seq_data = af.get_noah_RSA_values(pdb_id, chain_id) #Get the RSA info from DSSP
    RSAValues = []	
    RSA = seq_data[1]
    RSA_dict = seq_data[2]
    new_RSA = af.get_cut_RSA_values(pdb_id, RSA, RSA_dict) #Gets the RSA values that correspond to the sequence residues 
    index = 0

    natural_data_arr = cut_natural_sequences

    #filepointer for the partial result
    fpW_natural = open("results_array_natural_" + pdb_id + "_" + chain_id + ".csv","w")

    #write the RSA values:
    fpW_natural.write(af.dump_csv_line(new_RSA))

    [natural_sample1, natural_sample2] = af.split_natural_sequences(natural_data_arr) #Splits the sequences into two samples