diff --git a/mcsm_analysis/pyrazinamide/scripts/combining_two_df.R b/mcsm_analysis/pyrazinamide/scripts/combining_two_df.R
index 21559c2..31a533b 100644
--- a/mcsm_analysis/pyrazinamide/scripts/combining_two_df.R
+++ b/mcsm_analysis/pyrazinamide/scripts/combining_two_df.R
@@ -1,7 +1,7 @@
 #########################################################
 # TASK: To combine mcsm and meta data with af and or files  
 # Input csv files:
-# 1) mcsm output formatted
+# 1) mcsm normalised and struct params
 # 2) gene associated meta_data_with_AFandOR
 
 # Output: 
@@ -50,7 +50,8 @@ datadir = paste0('~/git/Data')
 # infile1: mCSM data
 #indir = '~/git/Data/pyrazinamide/input/processed/'
 indir = paste0(datadir, '/', drug, '/', 'output') # revised {TODO: change in mcsm pipeline}
-in_filename = 'mcsm_complex1_normalised.csv'
+#in_filename = 'mcsm_complex1_normalised.csv'
+in_filename = 'pnca_mcsm_struct_params.csv' 
 infile = paste0(indir, '/', in_filename)
 cat(paste0('Reading infile1: mCSM output file', ' ', infile) )
 
diff --git a/mcsm_analysis/pyrazinamide/scripts/combining_two_df_lig.R b/mcsm_analysis/pyrazinamide/scripts/combining_two_df_lig.R
index 0bce93c..361b6b6 100644
--- a/mcsm_analysis/pyrazinamide/scripts/combining_two_df_lig.R
+++ b/mcsm_analysis/pyrazinamide/scripts/combining_two_df_lig.R
@@ -3,6 +3,10 @@
 # by filtering for distance to ligand (<10Ang).
 # This script doesn't output anything.
 # This script is sourced from other .R scripts for plotting ligand plots
+
+# Input csv files:
+# 1) mcsm normalised and struct params
+# 2) gene associated meta_data_with_AFandOR
 #########################################################
 getwd()
 setwd('~/git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts/')
@@ -35,7 +39,8 @@ cat(gene_match)
 # infile1: mCSM data
 #indir = '~/git/Data/pyrazinamide/input/processed/'
 indir = paste0('~/git/Data', '/', drug, '/', 'output') # revised {TODO: change in mcsm pipeline}
-in_filename = 'mcsm_complex1_normalised.csv'
+#in_filename = 'mcsm_complex1_normalised.csv'
+in_filename = 'pnca_mcsm_struct_params.csv' 
 infile = paste0(indir, '/', in_filename)
 cat(paste0('Reading infile1: mCSM output file', ' ', infile) )