refine re dss script correction

[django_unres.git] / files / pbs8.csh

diff --git a/files/pbs8.csh b/files/pbs8.csh
index 31d7fb9..0e3867d 100755 (executable)
--- a/files/pbs8.csh
+++ b/files/pbs8.csh
@@ -73,16 +73,21 @@ rm ave
 
 #amber min refinement
 foreach i (`seq 1 5`)
-../files/refine.sh MODEL$i.pdb
+../files/refine.sh MODEL$i.pdb $ssbond
 end
 
 /users2/local/pymol_1.6/pymol -c ../files/model.pml
 
-/users2/local/bin/tmscore MODEL1.pdb plik.pdb > tmscore1.out
-/users2/local/bin/tmscore MODEL2.pdb plik.pdb > tmscore2.out
-/users2/local/bin/tmscore MODEL3.pdb plik.pdb > tmscore3.out
-/users2/local/bin/tmscore MODEL4.pdb plik.pdb > tmscore4.out
-/users2/local/bin/tmscore MODEL5.pdb plik.pdb > tmscore5.out
+awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' plik.pdb > tmp.pdb
+/users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp.pdb > plik1.pdb
+rm tmp.pdb
+
+/users2/local/bin/tmscore MODEL1.pdb plik1.pdb > tmscore1.out
+/users2/local/bin/tmscore MODEL2.pdb plik1.pdb > tmscore2.out
+/users2/local/bin/tmscore MODEL3.pdb plik1.pdb > tmscore3.out
+/users2/local/bin/tmscore MODEL4.pdb plik1.pdb > tmscore4.out
+/users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out
+rm plik1.pdb
 
 #END
 touch finished