X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;ds=sidebyside;f=files%2Fpbs8.csh;h=0e3867dba89f1824165dfccbbce729ae33d5fd0a;hb=e965db4a237f05d8ef5d1aa56b2494d1c54c067b;hp=2f412cca06a860c43eb42a585a513dd2c9d39423;hpb=78e8cb3f098dd1ac48d7036c1a27457dfee55663;p=django_unres.git

diff --git a/files/pbs8.csh b/files/pbs8.csh
index 2f412cc..0e3867d 100755
--- a/files/pbs8.csh
+++ b/files/pbs8.csh
@@ -72,17 +72,22 @@ ln -s file_wham_T*K_ave.pdb ave
 rm ave
 
 #amber min refinement
-foreach x (`seq 1 5`)
-../files/refine.sh MODEL$i.pdb
+foreach i (`seq 1 5`)
+../files/refine.sh MODEL$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