diff --git a/dynamut/dynamut_test.py b/dynamut/get_results.py
similarity index 100%
rename from dynamut/dynamut_test.py
rename to dynamut/get_results.py
diff --git a/dynamut/dynamut_reading_muts.py b/dynamut/reading_muts.py
similarity index 100%
rename from dynamut/dynamut_reading_muts.py
rename to dynamut/reading_muts.py
diff --git a/mcsm/run_mcsm.py b/mcsm/run_mcsm.py
index 7f29fd6..d23f8da 100755
--- a/mcsm/run_mcsm.py
+++ b/mcsm/run_mcsm.py
@@ -26,14 +26,14 @@ arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb fi
 arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
 
 # stage: submit, output url file
-arg_parser.add_argument('--url_file', help = 'Output results url file. The result of stage "submit". By default, it creates a output result url file in the output dir: "output_dir + gene.lower() + _result_urls.txt")
+arg_parser.add_argument('--url_file', help = 'Output results url file. The result of stage "submit". By default, it creates a output result url file in the output dir: "output_dir + gene.lower() + _result_urls.txt" ')
 
 # stage: get, intermediate mcsm output file
-arg_parser.add_argument('--outfile_scraped', help = 'Output mcsm results scraped.  The result of stage "get". By default, it creates an interim output file in the output dir: "output_dir + gene.lower() +_mcsm_output.csv")
+arg_parser.add_argument('--outfile_scraped', help = 'Output mcsm results scraped.  The result of stage "get". By default, it creates an interim output file in the output dir: "output_dir + gene.lower() +_mcsm_output.csv" ')
 
 # stage: format, formatted output with scaled values, etc
 # FIXME: Don't call this stage until you have ALL the interim results for your snps as the normalisation will be affected!
-arg_parser.add_argument('--outfile_formatted', help = 'Output mcsm results formatted.  The result of stage "format". By default, it creates a formatted output file in the output dir: "output_dir + gene.lower() + _complex_mcsm_norm.csv")
+arg_parser.add_argument('--outfile_formatted', help = 'Output mcsm results formatted.  The result of stage "format". By default, it creates a formatted output file in the output dir: "output_dir + gene.lower() + _complex_mcsm_norm.csv" ')
 
 arg_parser.add_argument('--debug', action='store_true', help = 'Debug Mode')
 
@@ -103,7 +103,7 @@ infile_pdb = indir + '/' + in_filename_pdb
 if mutation_filename:
     in_filename_snps = mutation_filename
 else:
-    in_filename_snps = gene.lower() + '_mcsm_snps.csv'
+    in_filename_snps = gene.lower() + '_mcsm_formatted_snps.csv'
     
 infile_snps = outdir + '/' + in_filename_snps
 
@@ -111,7 +111,7 @@ infile_snps = outdir + '/' + in_filename_snps
 # output
 #=======
 # mcsm_results globals
-if not result_url:
+if not result_urls:
     result_urls_filename = gene.lower() + '_result_urls.txt'
     result_urls =  outdir + '/' + result_urls_filename
     if DEBUG:
diff --git a/scripts/my_pdbtools/pdbtools b/scripts/my_pdbtools/pdbtools
index 881ff8f..eadbb22 160000
--- a/scripts/my_pdbtools/pdbtools
+++ b/scripts/my_pdbtools/pdbtools
@@ -1 +1 @@
-Subproject commit 881ff8f27aaf1db4266a84fb03baad3dab552c64
+Subproject commit eadbb223f3883be8730ba39e751a24f5ce0cd45d