diff --git a/scripts/aa_index_scripts/run_aaeg.sh b/scripts/aa_index_scripts/run_aaeg.sh
index 47bacbd..edf5fce 100755
--- a/scripts/aa_index_scripts/run_aaeg.sh
+++ b/scripts/aa_index_scripts/run_aaeg.sh
@@ -1,3 +1,18 @@
 #python /home/sportelli/Desktop/Important_Code/structural/aaindex/get_scores.py /home/sportelli/Desktop/Project_2_rpoB/leprae/RMLE_B_RFP.pdb C P28A
 #python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/pnca_complex.pdb A L4S
 python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A L4S
+
+# How I want it to run
+#drug = "pyrazinamide"
+#gene = "pncA" # force it to be lowercase
+#chain = "A"
+#mutfile = "/home/tanu/git/Data/output/<gene>_mcsm_snps.csv"
+#mut = for i in mutfile
+
+
+#$1 = "/home/tanu/git/Data/input/<gene>_complex.pdb
+#$2 = chain
+#$3 = mut
+
+#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py  $1 $2 $3
+