Custom peak list

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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 ...
 ...

Sequence read

sequence.read(file='Custom_model.txt', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)

Use awk to make a selected residues file

tcsh ;
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.

tcsh ;
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


See also