Re: error while running relax-GUI tutorial -- November 18, 2014 - 11:52

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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