Dear Prem.
Welcome to the mailing list!
I guess that you mean the manual at:
http://www.nmr-relax.com/manual/Contents.html
The relaxation dispersion auto-analysis in the GUI
http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html
Where the test data is in:
test_suite/shared_data/dispersion/Hansen
I will write it up here as a script instead.
This goes a little faster testing.
You can also find more inspiration at the wiki:
http://wiki.nmr-relax.com
http://wiki.nmr-relax.com/Category:Tutorials
In terminal
mkdir -p $HOME/test
cd $HOME/test
gedit test.py
Then I build the script onwards.
I run relax repeatedly, to execute code. Then I write new code in the
script, and run again.
relax test.py
When I am satisfied, you can then do like this.
relax -g -t log.txt
User functions -> Script -> test.py
THEN:
View -> Data pipe editor -> Right click on pipe -> Associate with a new
Auto analysis
This should bring you to a window, where all settings have been set.
Relaxations dispersion models: ['R2eff', 'No Rex', 'CR72', 'NS CPMG
2-site expanded']
Grid increements: 11 (For speed-up in test phase)
Monte-Carlo simulations number: 5 (For speed up in test phase)
Then a quick click on spin.isotope function, and GO.
test.py
----------------
#python modules
import os
import glob
# relax modules
from lib.io import sort_filenames
# Set path to data
data =
'/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/shared_data/dispersion/Hansen'
# Create the data pipe.
pipe_name = 'origin - relax_disp (Tue Nov 18 10:39:36 2014)'
pipe_bundle = 'relax_disp (Tue Nov 18 10:39:36 2014)'
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle,
pipe_type='relax_disp')
# Create spin to hold data.
sequence.read(file='fake_sequence.in', dir=data, res_num_col=1,
res_name_col=2)
deselect.read(file='unresolved', dir=data+os.sep+'500_MHz',
spin_id_col=None, mol_name_col=None, res_num_col=1, boolean='AND',
change_all=False)
deselect.read(file='unresolved', dir=data+os.sep+'800_MHz',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
boolean='AND', change_all=False)
# Give the spins attributes.
spin.isotope(isotope='15N', spin_id='@*', force=True)
spin.name(name='N')
# Do for 800.
###############################################
# Change directory.
os.chdir(data + os.sep + '500_MHz')
# Get the file list, and sort the file list Alphanumeric.
flist500 = glob.glob('*.in_sparky')
flist500 = sort_filenames(filenames=flist500)
# Make ID
ID500 = []
for f in flist500: ID500.append("500_"+f.split(".in_sparky")[0])
# Then Read
spectrum.read_intensities(file=flist500, spectrum_id=ID500)
# Repeat for the replicated spectra.
flist500rep = glob.glob('*in.bis_sparky')
flist500rep = sort_filenames(filenames=flist500rep)
# Make ID
ID500rep = []
for f in flist500rep:
ID500rep.append("500_"+f.split(".in.bis_sparky")[0]+'b')
# Then Read
spectrum.read_intensities(file=flist500rep, spectrum_id=ID500rep)
# Then map replicated
for b_id in ID500rep:
a_id = b_id[:-1]
spectrum.replicated(spectrum_ids=[a_id, b_id])
# Then check
print cdp.replicates
# Then repeat for 800.
###############################################
# Change directory.
os.chdir(data + os.sep + '800_MHz')
# Get the file list, and sort the file list Alphanumeric.
flist800 = glob.glob('*.in_sparky')
flist800 = sort_filenames(filenames=flist800)
# Make ID
ID800 = []
for f in flist800: ID800.append("800_"+f.split(".in_sparky")[0])
# Then Read
spectrum.read_intensities(file=flist800, spectrum_id=ID800)
# Repeat for the replicated spectra.
flist800rep = glob.glob('*in.bis_sparky')
flist800rep = sort_filenames(filenames=flist800rep)
# Make ID
ID800rep = []
for f in flist800rep:
ID800rep.append("800_"+f.split(".in.bis_sparky")[0]+'b')
# Then Read
spectrum.read_intensities(file=flist800rep, spectrum_id=ID800rep)
# Then map replicated
for b_id in ID800rep:
a_id = b_id[:-1]
spectrum.replicated(spectrum_ids=[a_id, b_id])
# Then check
print cdp.replicates
################################################
print len(ID500), len(ID500rep), len(ID800), len(ID800rep)
# Then set spectrum properties
all_ID = ID500 + ID500rep + ID800 + ID800rep
for cur_id in all_ID:
# Split from name
sfrq_str, vcpmg_str = cur_id.split("_")
if vcpmg_str == 'reference':
vcpmg = None
else:
vcpmg = float(vcpmg_str.split("b")[0])
print cur_id, sfrq_str, vcpmg
# Set the current experiment type.
relax_disp.exp_type(spectrum_id=cur_id, exp_type='SQ CPMG')
# Set the NMR field strength of the spectrum.
spectrometer.frequency(id=cur_id, frq=float(sfrq_str), units='MHz')
# Relaxation dispersion CPMG constant time delay T (in s).
relax_disp.relax_time(spectrum_id=cur_id, time=0.03)
# Set the relaxation dispersion CPMG frequencies.
relax_disp.cpmg_setup(spectrum_id=cur_id, cpmg_frq=vcpmg)
-------------------------------------------------------
2014-11-18 0:06 GMT+01:00 Prem Raj Joseph <prbj123relax@xxxxxxxxx>:
Hello all,
I was using the GUI version of the software to run the tutorial
available
in the manual for analysis of relaxation dispersion.
When i execute the run I get the following error
RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Mon Nov
17
10:50:08 2014)' already exists.
Not sure where the error is arising from. Any help is greatly
appreciated.
Thanks
Prem
Department of Biochemistry and Molecular Biology
Sealy Center for Structural Biology and Molecular Biophysics
5.142 Medical Branch Building
University of Texas Medical Branch
Galveston, TX 77555-1055
Lab: 409-772-2181
Cell: 409-354-8536
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Error analysis
==============
Skipping the error analysis as it has already been performed.
relax> relax_disp.r1_fit(fit=False)
---------------------
- The 'R2eff' model -
---------------------
relax> pipe.copy(pipe_from='origin - relax_disp (Mon Nov 17 10:50:08
2014)', pipe_to='R2eff - relax_disp (Mon Nov 17 10:50:08 2014)',
bundle_to='relax_disp (Mon Nov 17 10:50:08 2014)')
Exception raised in thread.
Traceback (most recent call last):
File "/home/prem/programs/relax-3.3.2/gui/analyses/execute.py", line
87,
in run
self.run_analysis()
File
"/home/prem/programs/relax-3.3.2/gui/analyses/auto_relax_disp.py",
line 726, in run_analysis
Relax_disp(pipe_name=self.data.pipe_name,
pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir,
models=self.data.models, grid_inc=self.data.inc,
mc_sim_num=self.data.mc_sim_num,
exp_mc_sim_num=self.data.exp_mc_sim_num,
pre_run_dir=self.data.pre_run_dir,
mc_sim_all_models=self.data.mc_sim_all_models,
insignificance=self.data.insignificance,
numeric_only=self.data.numeric_only, r1_fit=self.data.r1_fit)
File "/home/prem/programs/relax-3.3.2/auto_analyses/relax_disp.py",
line
137, in __init__
self.run()
File "/home/prem/programs/relax-3.3.2/auto_analyses/relax_disp.py",
line
614, in run
self.interpreter.pipe.copy(pipe_from=self.pipe_name,
pipe_to=model_pipe, bundle_to=self.pipe_bundle)
File "/home/prem/programs/relax-3.3.2/prompt/uf_objects.py", line
225, in
__call__
self._backend(*new_args, **uf_kargs)
File "/home/prem/programs/relax-3.3.2/pipe_control/pipes.py", line
191,
in copy
raise RelaxPipeError(pipe_to)
RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Mon Nov
17
10:50:08 2014)' already exists.
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