diff --git a/foldx/runFoldx.py b/foldx/runFoldx.py
index d8ad130..50ea562 100755
--- a/foldx/runFoldx.py
+++ b/foldx/runFoldx.py
@@ -68,9 +68,9 @@ pdb_filename    = args.pdb_file
 # Just the filename, thanks
 #pdb_name = Path(in_filename_pdb).stem
 
-#==========
-# dir
-#==========
+#============
+# directories
+#============
 if data_dir:
     datadir = data_dir
 else:
diff --git a/mcsm/run_mcsm.py b/mcsm/run_mcsm.py
index 587cc44..8434091 100755
--- a/mcsm/run_mcsm.py
+++ b/mcsm/run_mcsm.py
@@ -15,8 +15,8 @@ arg_parser.add_argument('-s', '--stage',   help='mCSM Pipeline Stage', default =
 arg_parser.add_argument('-H', '--host',    help='mCSM Server', default = 'http://biosig.unimelb.edu.au')
 arg_parser.add_argument('-U', '--url',     help='mCSM Server URL', default = 'http://biosig.unimelb.edu.au/mcsm_lig/prediction')
 arg_parser.add_argument('-c', '--chain',   help='Chain ID as per PDB, Case sensitive', default = 'A')
-arg_parser.add_argument('-l','--ligand',   help='Ligand ID as per PDB, Case sensitive. REQUIRED only in "submit" stage')
-arg_parser.add_argument('-a','--affinity', help='Affinity in nM', default = 0.99) 
+arg_parser.add_argument('-l','--ligand',   help='Ligand ID as per PDB, Case sensitive. REQUIRED only in "submit" stage', default = None)
+arg_parser.add_argument('-a','--affinity', help='Affinity in nM. REQUIRED only in "submit" stage', default = 0.99) 
 arg_parser.add_argument('-pdb','--pdb_file', help = 'PDB File') 
 arg_parser.add_argument('--datadir', help = 'Data Directory')
 arg_parser.add_argument('--debug', action='store_true', help = 'Debug Mode')
@@ -48,6 +48,9 @@ homedir = os.path.expanduser('~')
 #os.chdir(homedir + '/git/LSHTM_analysis/mcsm')
 gene_match = gene + '_p.'
 
+#============
+# directories
+#============
 if data_dir:
     datadir = data_dir
 else:
@@ -56,6 +59,9 @@ else:
 indir = datadir + '/' + drug + '/' + 'input'
 outdir = datadir + '/' + drug + '/' + 'output'
 
+#=======
+# input
+#=======
 if pdb_filename:
     in_filename_pdb = pdb_filename
 else:
@@ -66,6 +72,9 @@ infile_pdb = indir + '/' + in_filename_pdb
 in_filename_snps = gene.lower() + '_mcsm_snps.csv' #(outfile_mcsm_snps, from data_extraction.py)
 infile_snps = outdir + '/' + in_filename_snps
 
+#=======
+# output
+#=======
 # mcsm_results globals
 result_urls_filename = gene.lower() + '_result_urls.txt'
 result_urls =  outdir + '/' + result_urls_filename
diff --git a/scripts/dssp_df.py b/scripts/dssp_df.py
index bd4d910..3d5dfcd 100755
--- a/scripts/dssp_df.py
+++ b/scripts/dssp_df.py
@@ -60,9 +60,9 @@ pdb_filename = args.pdb_file
 
 DEBUG        = args.debug
 
-#==========
-# dirs
-#==========
+#=============
+# directories
+#=============
 if data_dir:
     datadir = data_dir
 else:
@@ -204,8 +204,8 @@ def dssp_to_csv(inputdsspfile, outfile, pdbchainlist = ['A']):
 #=======================================================================
 def main():
     print('Running dssp with the following params:\n'
-		, '\ninput pdb:', in_filename_pdb
-		, '\noutfile:', out_filename_dssp_csv)
+		, '\nInput pdb file:', in_filename_pdb
+		, '\nOutput:', out_filename_dssp_csv)
     dssp_file_from_pdb(infile_pdb, dssp_file, DSSP = "dssp")
     my_chains = extract_chain_dssp(infile_pdb)
     dssp_to_csv(dssp_file, outfile_dssp_csv, my_chains)