Difference between revisions of "Custom peak list"

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== Select residues ==
 
== Select residues ==
<source lang="text">
+
<source lang="bash">
 
set IN=table_ser_files_model.txt ;
 
set IN=table_ser_files_model.txt ;
 
set SELRESIS=sel_resi.txt ;
 
set SELRESIS=sel_resi.txt ;
Line 22: Line 22:
 
</source>
 
</source>
 
After this step, you should remove those lines with residues you dont want to have in the new file.
 
After this step, you should remove those lines with residues you dont want to have in the new file.
<source lang="text">
+
<source lang="bash">
 
set IN=table_ser_files_model.txt ;
 
set IN=table_ser_files_model.txt ;
 
set SELRESIS=sel_resi.txt ;
 
set SELRESIS=sel_resi.txt ;

Revision as of 09:00, 17 June 2013

Custom peak list

protein 3 R 3 N 3.642647e+06 6.056554e+06 3.753433e+06 ...
protein 5 E 5 N 1.609356e+06 2.927111e+06 1.726433e+06 ...
protein 6 V 6 N 1.697771e+06 3.015788e+06 1.771777e+06 ...
protein 7 N 7 N 1.535896e+06 3.005234e+06 1.683477e+06 ...
protein 8 I 8 N 1.332059e+06 2.611723e+06 1.519182e+06 ...
protein 9 V 9 N 1.532644e+06 2.834876e+06 1.597882e+06 ...
protein 11 N 11 N 1.219399e+06 2.479556e+06 1.289455e+06 ...
protein 15 D 15 N 2.808704e+06 4.812759e+06 2.935094e+06 ...
protein 16 Q 16 N 3.410860e+06 5.823456e+06 3.427248e+06 ...
protein 22 E 22 N 3.681818e+06 6.378086e+06 3.663392e+06 ...
 ...

Select residues

set IN=table_ser_files_model.txt ;
set SELRESIS=sel_resi.txt ;
awk '{print $2}' $IN > $SELRESIS ;
gedit $SELRESIS

After this step, you should remove those lines with residues you dont want to have in the new file.

set IN=table_ser_files_model.txt ;
set SELRESIS=sel_resi.txt ;
set RESIS=`cat $SELRESIS` ;
set DATE=`date '+%Y%m%d_%H%M'` ;
set TMP=${IN}_${DATE} ;
cp $IN $TMP ;
rm $IN ;
set T=$ ;
echo $RESIS ;
foreach RESI ($RESIS) ;
cat  $TMP | awk "{if (${T}2 == $RESI ) { print ${T}0; } }" >> $IN
end ;
cat $IN ;

Make an execution script

Start relax GUI with logfile

relax_disp -g -l LOGFILE.txt