Tutorial for R1/R2 Relaxation curve-fitting analysis on varian recorded as fid interleaved

Intro

Made from Tutorial for Relaxation dispersion analysis cpmg fixed time recorded on varian as fid interleaved

Get the process helper scripts

1. stPeakList.pl

Check the peak list matches

Check the peak list matches

sparky 0/test.ucsf

Prepare files

Make standard peak list

stPeakList.pl 0/test.ft2 peak_list_SPARKY.list > peak_list_SPARKY.tab
cat peak_list_SPARKY.tab

Find *.ft2 files

ls -v -d -1 */*.ft2 > ft2_files.ls
cat ft2_files.ls

Measure heights

seriesTab -in peak_list_SPARKY.tab -out peaks_list_max_standard.ser -list ft2_files.ls -max
cat peaks_list_max_standard.ser

Extract the spectra settings from Varian procpar file

set RELAXT=`awk '/^relaxT /{f=1;next}f{print $0;exit}' procpar`; echo $NCYCLIST
set SFRQ=`awk '/^sfrq /{f=1;next}f{print $2;exit}' procpar`; echo $SFRQ

foreach I (`seq 2 ${#RELAXT}`)
  set T=${RELAXT[$I]}; echo $T $SFRQ >> relaxt.txt
end

cat relaxt.txt

Measure RMSD in spectra

Measure the backgorund noise RMSD in each of the .ft2 files

Very fast way - RMSD via nmrpipe showApod

We can also use the showApod rmsd.

set FIDS=`cat ft2_files.ls`
set OUT=${PWD}/apod_rmsd.txt
set CWD=$PWD
rm $OUT

foreach I (`seq 1 ${#FIDS}`)
set FID=${FIDS[$I]}; set DIRN=`dirname $FID`
cd $DIRN
set apodrmsd=`showApod *.ft2 | grep "REMARK Automated Noise Std Dev in Processed Data:" | awk '{print $9}'`
echo $apodrmsd $DIRN >> $OUT
cd $CWD
end
cat $OUT

paste relaxt.txt $OUT > settings.txt

Relax script

File: relax_1_ini.py

import os
from auto_analyses.relax_fit import Relax_fit

# Taken from the relax disp manual, section 10.6.1 Dispersion script mode - the sample script
# Create the data pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_fit'
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_fit')
 
# Create the spins
spectrum.read_spins(file='peaks_list_max_standard.ser', dir=None)
 
# Read the spectrum from NMRSeriesTab file. The "auto" will generate spectrum name of form: Z_A{i}
spectrum.read_intensities(file="peaks_list_max_standard.ser", dir=None, spectrum_id='auto', int_method='height')
 
# Loop over the spectra settings.
timesfile=open('settings.txt','r')
 
i = 0
for line in timesfile:
    timeT = line.split()[0]
    set_sfrq = float(line.split()[1])
    rmsd_err = float(line.split()[2])
 
    print timeT, set_sfrq, rmsd_err
 
    # Set the current spectrum id
    current_id = "Z_A%s"%(i)

    # Set the relax time
    relax_fit.relax_time(time=float(timeT), spectrum_id=current_id)

    # Set the peak intensity errors, as defined as the baseplane RMSD.
    spectrum.baseplane_rmsd(error=rmsd_err, spectrum_id=current_id)
 
    i += 1
 
# Save the program state before run.
# This state file will also be used for loading, before a later cluster/global fit analysis.
state.save('ini_setup', force=True)

# Set settings for run.
results_directory = os.path.join(os.getcwd(),"model_sel_analyt")
pipe_name = 'base pipe'; pipe_bundle = 'relax_fit'
#GRID_INC = 11; MC_NUM = 500
GRID_INC = 21; MC_NUM = 100

Relax_fit(pipe_name=pipe_name, pipe_bundle=pipe_bundle, file_root='rx', results_dir=results_directory, grid_inc=GRID_INC, mc_sim_num=MC_NUM, view_plots=True)

Analyse

relax_trunk relax_1_ini.py -t log_relax_1_ini.log