Difference between revisions of "Custom peak list"

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__TOC__
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== Custom peak list ==
 
== Custom peak list ==
 
<source lang="text">
 
<source lang="text">
protein 3 R 3 N 3.642647e+06 6.056554e+06 3.753433e+06
+
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 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 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 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 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 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 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 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 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
+
protein 22 E 22 N 3.681818e+06 6.378086e+06 3.663392e+06 ...
 +
...
 
</source>
 
</source>
  
=== Select residues ===
+
== Sequence read ==
<source lang="text">
+
<source lang="python">
 +
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)
 +
</source>
 +
 
 +
== Use awk to make a selected residues file ==
 +
<source lang="bash">
 +
tcsh ;
 
set IN=table_ser_files_model.txt ;
 
set IN=table_ser_files_model.txt ;
 
set SELRESIS=sel_resi.txt ;
 
set SELRESIS=sel_resi.txt ;
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</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">
 +
tcsh ;
 
set IN=table_ser_files_model.txt ;
 
set IN=table_ser_files_model.txt ;
 
set SELRESIS=sel_resi.txt ;
 
set SELRESIS=sel_resi.txt ;
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</source>
 
</source>
  
 +
== Make an execution script ==
 +
 +
== Start relax GUI with logfile ==
 
  relax_disp -g -l LOGFILE.txt
 
  relax_disp -g -l LOGFILE.txt
 +
 +
 +
= See also =
 +
 
[[Category:Peak_lists]]
 
[[Category:Peak_lists]]
 +
[[Category:Relaxation]]
 +
[[Category:Relaxation dispersion analysis]]
 +
[[Category:Relaxation_rates]]
 +
[[Category:Steady-state NOE analysis]]

Latest revision as of 13:46, 15 October 2015

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