setenv numstruc `grep ENERGY tmp.pdb|wc -l`
setenv allline `cat tmp.pdb|wc -l`
setenv onestruc `echo $allline "/" $numstruc| bc -l|sed 's/\.0*//'`
- foreach i (2 4 6 8 10)
+ foreach i (`seq 2 2 $numstruc`)
setenv headval `echo $i "*" $onestruc|bc -l`
setenv halfi `echo $i/2|bc`
head -n $headval tmp.pdb | tail -n $onestruc >MODEL${halfi}.pdb
else
# proteins with L-aminoacids only
ln -s file_wham_T*K_ave.pdb ave
+setenv numstruc `awk '/ENERGY/{i++}END{print i/2}' ave`
../files/cluster2allatom.sh ave
rm ave
#amber min refinement
-foreach i (`seq 1 5`)
+foreach i (`seq 1 $numstruc`)
../files/refine.sh MODEL$i.pdb $ssbond
end
endif
grep -v TER plik1ter.pdb | awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' > tmp.pdb
/users2/local/mmtsb/perl/convpdb.pl -setchain A -renumber 1 -out generic_noh plik.pdb |grep ATOM > plik1chain.pdb
/users2/local/mmtsb/perl/convpdb.pl -setchain B -renumber 1 -out generic_noh plik2.pdb |grep ATOM >> plik1chain.pdb
- foreach i (`seq 1 5`)
+ foreach i (`seq 1 $numstruc`)
sed /TER/q MODEL$i.pdb_ > tmp1.pdb
/users2/local/mmtsb/perl/convpdb.pl -setchain A -renumber 1 -out generic_noh tmp1.pdb |grep ATOM > MODEL${i}chain.pdb
sed '0,/TER/d' MODEL$i.pdb_ > tmp2.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
+ foreach i (`seq 1 $numstruc`)
+ /users2/local/bin/tmscore MODEL${i}.pdb plik1.pdb > tmscore${i}.out
+ end
if (-e saxs.data) then
awk -f ../files/saxs_dist.awk plik1.pdb > plik_saxs.data
endif
endif
if (-e saxs.data) then
-awk -f ../files/saxs_dist.awk MODEL1.pdb > MODEL1_saxs.data
-awk -f ../files/saxs_dist.awk MODEL2.pdb > MODEL2_saxs.data
-awk -f ../files/saxs_dist.awk MODEL3.pdb > MODEL3_saxs.data
-awk -f ../files/saxs_dist.awk MODEL4.pdb > MODEL4_saxs.data
-awk -f ../files/saxs_dist.awk MODEL5.pdb > MODEL5_saxs.data
+foreach i (`seq 1 $numstruc`)
+awk -f ../files/saxs_dist.awk MODEL${i}.pdb > MODEL${i}_saxs.data
+end
../files/plot_saxs.py
endif