refine re dss script correction

diff --git a/TODO b/TODO
index 7e57796..b071ca4 100644 (file)
--- a/TODO
+++ b/TODO
@@ -25,6 +25,8 @@ homology restraints input
 
 other restrains input
 
+automatic secondary structure restrains (psipred)
+
 MREMD - add cluster parameters, change after run and rerun only cluster analysis
       - button to make movie from selected trajectory after run
 

diff --git a/files/refine.sh b/files/refine.sh
index f004597..65f9274 100755 (executable)
--- a/files/refine.sh
+++ b/files/refine.sh
@@ -35,7 +35,7 @@ $AMBERHOME/bin/tleap -f leap.bat
 
 /users2/local/mmtsb/perl/convpdb.pl -out generic_noh z_tleap.pdb > noh.pdb
 /users2/local/pymol_1.6/pymol -cq /users2/CASP12/EXAMPLES/all-atom/amber_files/dss.py | awk \
-'{ires[NR]=$2;ss[NR]=$3}END{for (i=2;i<=NR;i++) {if (ss[i-1]!=ss[i]&&ss[i-1]=="L") printf "%s;",ires[i];if (ss[i-1]!=ss[i]&&ss[i]=="L") printf "%s;%s\n",ires[i-1],ss[i-1]}}' \
+'{ires[NR]=$2;ss[NR]=$3}END{for (i=2;i<=NR;i++) {if (ss[i-1]!=ss[i]&&ss[i-1]!="L") printf "%s;%s\n",ires[i-1],ss[i-1];if (ss[i-1]!=ss[i]&&ss[i]!="L") printf "%s;",ires[i];}}' \
 > zakresy.csv