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__TOC__
= Intro =
This tutorial is based on the analysis of NMR data from the paper:
<blockquote>
== Spectral processing ==
== Fourier transform all spectra ==
As stated in the [[manual | relax manual]] section '''5.2.1 Temperature control and calibration''', the pulse sequence can put a lot of power into the sample. <br>
You could read these sections in the relax manual: <br>[http://www.nmr-relax.com/manual/Temperature_control_calibration.html Importance of Temperature control and calibration]<br>[http://www.nmr-relax.com/manual/relax_data_temp_control.html Temperature control]<br>[http://www.nmr-relax.com/manual/relax_data_temp_calibration.html Temperature calibration]<br> It is therefore good also good practice to inspect for peak movements, by overlaying all spectra:
Open all the files, and overlay them with SPARKY command '''ol'''.
= Analyse in relax =
== Extract the spectra settings from Varian procpar file ==
== Measure the backgorund noise "RMSD" in each of the .ft2 files ==
=== RMSD via sparky ===
There exist two ways to get the background RMSD noise
0 0.06 0 599.8908622 2.39e+03
24 0.06 400.00000000000000000000 599.8908622 2.45e+03
</source>
=== RMSD via nmrpipe showApod ===
We can also use the showApod rmsd.
<source lang="bash">
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
mv ncyc.txt ncyc_or.txt
paste ncyc_or.txt $OUT > ncyc.txt
</source>
cp ncyc.txt ../relax
cp peaks_list* ../relax
cd ../relax
</source>
# Set the current spectrum id
current_id = "Z_A%s"%(i)
# Set the current experiment type.
relax_disp.exp_type(spectrum_id=current_id, exp_type='SQ CPMG')
# Set the peak intensity errors, as defined as the baseplane RMSD.
# Set the NMR field strength of the spectrum.
spectrometer.frequency(id=current_id, frq=set_sfrq, units=‘MHz’'MHz')
# Relaxation dispersion CPMG constant time delay T (in s).
# Set the relaxation dispersion CPMG frequencies.
relax_disp.cpmg_frqcpmg_setup(spectrum_id=current_id, cpmg_frq=vcpmg)
i += 1
# Ctrl+n for new analysis
# Select '''Relaxation dispersion analysis''' button -> Next
# Starting pipe: '''base pipe'''
# Pipe bundle: '''relax_disp''' -> Start
# The file name: '''peaks_list_max_standard.ser'''
# The spectrum ID string: auto
# Leave the rest of the fields as they are, they are not used.
# Push "Apply" and then '''Cancel'''
# We want to change the spectra properties by a script.
# Point '''Results directory''' to '''model_sel_analyt'''.
# Set Monte-Carlo Simulations to '''10'''
# Select models: Lets take '''"R2eff", "No Rex", "TSMFK01", "LM63", "CR72", "CR72 full", "IT99"'''
# Save the state again, so the settings for models, monte-carlo settings and result directory is preserved.
# Shift+Ctrl+s OR File-> Save as... '''ini_run.bz2''' in the '''model_sel_analyt''' directory.
# Now push "Execute"
The analysis will probably take between 4-10 hours.<br>
=== Analyse via script ===
pipe_bundle = 'relax_disp'
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
# Create the spins
# Name the isotope for field strength scaling.
results_directory = os.path.join(os.getcwd(),"model_sel_analyt")
pipe_name = 'base pipe'; pipe_bundle = 'relax_disp'
MODELS = ['R2eff', 'No Rex', 'TSMFK01', 'LM63', 'CR72', 'CR72 full', 'IT99']
GRID_INC = 21; MC_NUM = 10; MODSEL = 'AIC'
relax_disp relax_4_model_sel.py -t log_relax_4_model_sel.log
</source>
The analysis will probably take between 4-10 hours.<br>
== Rerun from a "ini_setup.bz2" file ==
After the analysis, several folders should be available, with data for each fitted model.
<source lang="bash">
R2eff/
No Rex/
TSMFK01/
LM63/
CR72/
CR72 full/
IT99/
final/
</source>
You can convert all to PNG images, by:
<source lang="bash">
cd "R2eff"; ./grace2images.py; cd .. ;
cd "No Rex"; ./grace2images.py; cd .. ;
cd "TSMFK01"; ./grace2images.py; cd .. ;
cd "LM63"; ./grace2images.py; cd .. ;
cd "CR72"; ./grace2images.py; cd .. ;
cd "CR72 full"; ./grace2images.py; cd .. ;
cd "IT99"; ./grace2images.py; cd .. ;
cd "final"; ./grace2images.py; cd .. ;
find . -type f -name "*.png"
See [[Grep_log_file]] for this.
== Inspect model selection Compare values ==For the '''TSMFK01''' and for example the '''CR72''', the '''k_AB''' value can be compare
<source lang="bash">cd model_sel_analytpaste "TSMFK01/k_AB.out" "CR72/k_AB.out" | awk '{print $2, $3, $6, $13}'</source> == With Inspect model selection for residues == === Grep AIC selection from logfile ===
If you have a log file.
<source lang="bash">
set IN=log_relax_4_model_sel.log ;
set OUT=log_relax_4_model_sel_chosen_models.log txt ;
set FROM=`grep -n "AIC model selection" $IN | cut -d":" -f1` ;
</source>
=== In relax prompt get spin.model ===
See [[:Category:List_objects]] to get inspiration how to loop through the data class containers.
Select a spin, and look for the Variable '''model'''.
All spins of one cluster ID will be optimised as one model. <br>
Several cluster ID will result in all those spins being optimised separately, but again with all spins together. <br>
and the function '''specific_analyses.relax_disp.disp_data.loop_cluster''' which it uses.
Let us select residues based on a criterion where the highest number of residues have been fitted to the same model.
Open the '''final_state.bz2''' in relax GUI. <br>
You can see the model select for each residue in the '''Spin viewer''' (View -> Spin viewer (Ctrl+T)). Look for the '''Variable''' '''model'''.
Open the relax prompt with '''Ctrl+p''' if you are in the GUI.<br>
<source lang="python">
from pipe_control.mol_res_spin import spin_loop
# Open file for writing
cluster_file = "cluster_residues.txt"
f = open(cluster_file, 'w')
# Make a list to count number of models
resi_models = []
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True): # Write models to file f.write( str(spin_id) + " ; " + str(spin.model) + " ; " + str(mol_name) + " ; " + str(res_num) + " ; " + str(res_name) + "\n" ) # Append models to list
resi_models.append(spin.model)
# Count resi_models
#Close the file
f.close()
</source>
For the clustered analysis, you need to start a new analysis. <br>
You should not load the results from the final pipe, since this will likely be fatal for the clustered analysis. <br>
So Close relax, and then add these files.
=== Analyse Do clustering Analysis in GUI ===
Start relax in GUI mode
<source lang="python">
relax_disp -g -t log_relax_6_clusterlog_relax_5_cluster.log
</source>
# Open the '''ini_setup.bz2 ''' from File->"Open relax state".
# Open the '''relax prompt''' with '''Ctrl+p'''. And paste this is.
<source lang="python">
# Cluster residues
cluster_file = "cluster_residues.txt"
f = open(cluster_file, 'r')
for line in f:
f.close()
# Check which are clusteredprint cdp.clustering # Check for selected/deselected spins.for spin, spin_id in spin_loop(return_id=True, skip_desel=False): print spin_id, spin.select
</source>
# Before executing, it would be a good idea to save the state after clustering.
# Shift+Ctrl+s OR File-> Save as... '''ini_setup_cluster.bz2'''
# Ctrl+d , right click "base pipe" and "Associate with a new auto-analysis"
# Close pipe viewer
# Make a directory for the output of the results, f.ex: '''model_clustering_analyt'''
# Point '''Results directory''' to '''model_clustering_analyt'''.
# Pint '''Previous run directory''' to previous result directory, where all the models had their folders. Values will be read from here. '''model_sel_analyt'''
# Set Monte-Carlo Simulations to '''1050'''# Select models: Lets take '''"R2eff", "No Rex", "CR72TSMFK01", "IT99"'''# Save the state again, so the settings for models, monte-carlo settings and result directorys is preserved.# Shift+Ctrl+s OR File-> Save as... '''ini_run_cluster.bz2''' in the '''model_clustering_analyt''' directory.
# Now push "Execute"
==== Analyse cluster via Do clustering Analysis in script ====
Add the following python relax script file to the relax directory.
'''relax_5_ini_clusterrelax_5_cluster.py'''
<source lang="python">
"""Taken from the relax disp manual, section 10.6.1 Dispersion script mode - the sample script.
To run the script, simply type:
$ ../../../../../relax relax_5_cluster.py --tee relax_5_cluster.log
"""
import os
from auto_analyses.relax_disp import Relax_disp
from pipe_control.mol_res_spin import spin_loop
# Set settings for run.
pre_run_directory = os.path.join(os.getcwd(),"model_sel_analyt")
results_directory = os.path.join(os.getcwd(),"model_clustering_analyt")
cluster_file = "cluster_residues.txt"
# Load the previous final state with results.
state.load(state='final_state.bz2', dir=pre_run_directory, force=False)
# Open file for writing
f = open(cluster_file, 'w')
# Make a list to count number of models
resi_models = []
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
# Write models to file
f.write( str(spin_id) + " ; " + str(spin.model) + " ; " + str(mol_name) + " ; " + str(res_num) + " ; " + str(res_name) + "\n" )
# Append models to list
resi_models.append(spin.model)
# Count resi_models
c_resi_models = dict((i,resi_models.count(i)) for i in resi_models)
print c_resi_models
# Write count result to file
for key, val in c_resi_models.items():
f.write( "# ; " + str(key) + " ; " + str(val) + "\n" )
# Load Close the initial state setupfile statef.loadclose(state='ini_setup.bz2')
##################
# Cluster file for selection residues.
# Cluster residues
f = open(cluster_file, 'r')
for line in f:
f.close()
# Check which are clustered
print cdp.clustering # Check for selected/deselected spins.for spin, spin_id in spin_loop(return_id=True, skip_desel=False): print spin_id, spin.select
# Save the program state before run.
state.save('ini_setup_cluster.bz2', force=True)
# Set settings for run.
pipe_name = 'base pipe'; pipe_bundle = 'relax_disp'
MODELS = ['R2eff', 'No Rex', 'CR72', 'IT99TSMFK01']GRID_INC = 21; MC_NUM = 1050; MODSEL = 'AIC'
# Execute
And the just start relax with
<source lang="bash">
relax_disp relax_5_ini_clusterrelax_5_cluster.py -t log_relax_5_ini_cluster.logrelax_disp relax_6_cluster.py -t log_relax_6_clusterlog_relax_5_cluster.log
</source>
= See also =
[[Category:Relaxation dispersion analysis]]
[[Category:Tutorials]]