Dear Atul.
Please use the support tracker when you upload files.
The email list is fragile, and cannot handle email attachment.
I made small modifications to your script.
I normally split them up.
1st script for setup, and printing stuff to check.
2nd script, which just call the previous script, and run analysis.
So, I would:
relax 1_setup_r1rho.py
to check everything.
When I am happy, I just:
relax 2_pre_run_r2eff.py
which call script 1, setup, and then run.
Did you know you can also:
relax 1_setup_r1rho.py -p
This runs the script, and enters terminal. Like "python -i script.py"
Any variable saved in the "cdp" can be accessed.
Try:
relax 1_setup_r1rho.py -p
print cdp.temp
You can also run relax with the debug option "-d"
relax 2_pre_run_r2eff.py -d
This gives more information about where the error is.
Anyway.
The problem seems related to, that you only have one reference
intensity per offset.
----1_setup_r1rho.py
# Python module imports.
from os import sep, getcwd
# relax module imports.
from pipe_control.mol_res_spin import generate_spin_string,
return_spin, spin_loop
from specific_analyses.relax_disp.data import average_intensity,
generate_r20_key, get_curve_type, has_exponential_exp_type,
has_r1rho_exp_type, loop_exp_frq, loop_exp_frq_offset_point,
loop_exp_frq_offset_point_time, loop_time, return_grace_file_name_ini,
return_param_key_from_data
# Set up the data pipe.
#######################
# The path to the data files.
DATA_PATH = getcwd()
# Create the data pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
# Read the spins from a spectum file instead. This already contain the
spin name.
spectrum.read_spins(file='2100_off_reso_R1rho.list', dir=DATA_PATH)
# Set the isotope information.
spin.isotope(isotope='15N')
# Loop over spins, to see current setup.
for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
print mol_name, resi, resn, spin_id
print " "
print cur_spin
# The spectral data - spectrum ID, peak list file name, spin-lock
field strength (Hz), the spin-lock offset (ppm), the relaxation time
(s), spectrometer frequency (Hz), and experimental error (RMSD of the
base plane noise for each spectrum).
data = [
['ref_off_reso_R1rho', 'ref_off_reso_R1rho.list', None, 150.87,
0.320, 900.21422558574e6, 90000.0],
['2100_off_reso_R1rho', '2100_off_reso_R1rho.list', 1500.0,
141.01, 0.320, 900.21422558574e6, 90000.0],
['2728_off_reso_R1rho', '2728_off_reso_R1rho.list', 1500.0,
147.89, 0.320, 900.21422558574e6, 90000.0],
['3357_off_reso_R1rho', '3357_off_reso_R1rho.list', 1500.0,
154.78, 0.320, 900.21422558574e6, 90000.0],
['3985_off_reso_R1rho', '3985_off_reso_R1rho.list', 1500.0,
161.66, 0.320, 900.21422558574e6, 90000.0],
['4614_off_reso_R1rho', '4614_off_reso_R1rho.list', 1500.0,
168.55, 0.320, 900.21422558574e6, 90000.0],
['5242_off_reso_R1rho', '5242_off_reso_R1rho.list', 1500.0,
175.43, 0.320, 900.21422558574e6, 90000.0],
['5871_off_reso_R1rho', '5871_off_reso_R1rho.list', 1500.0,
182.32, 0.320, 900.21422558574e6, 90000.0],
['6500_off_reso_R1rho', '6500_off_reso_R1rho.list', 1500.0,
189.21, 0.320, 900.21422558574e6, 90000.0]
]
# Loop over the spectra.
for id, file, field, offset, relax_time, H_frq, rmsd in data:
print("\n###############")
print("id=%s, field=%s, offset=%3.2f, time=%1.3f, frq=%3.1f,
rmsd=%3.2f" % (id, field, offset, relax_time, H_frq/1e6, rmsd) )
# Load the peak intensities and set the errors.
spectrum.read_intensities(file=file, dir=DATA_PATH,
spectrum_id=id, int_method='height')
spectrum.baseplane_rmsd(spectrum_id=id, error=rmsd)
# Set the relaxation dispersion experiment type.
relax_disp.exp_type(spectrum_id=id, exp_type='R1rho')
# Set the relaxation dispersion spin-lock field strength (nu1).
relax_disp.spin_lock_field(spectrum_id=id, field=field)
# Set the spin-lock offset.
relax_disp.spin_lock_offset(spectrum_id=id, offset=offset)
# Set the relaxation times (in s).
relax_disp.relax_time(spectrum_id=id, time=relax_time)
# Set the NMR field strength of the spectrum.
spectrometer.frequency(id=id, frq=H_frq)
# Load the R1 data.
relax_data.read(ri_id='R1', ri_type='R1', frq=H_frq,
file='R1_relax.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6,
error_col=7)
# Read the chemical shift data.
chemical_shift.read(file='2100_off_reso_R1rho.list', dir=DATA_PATH)
# Loop over spins, to see current setup.
for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
print mol_name, resi, resn, spin_id
print " "
print cur_spin
print " "
# Loop over setup.
for id in cdp.exp_type.keys():
print id, cdp.exp_type[id], cdp.spectrometer_frq[id],
cdp.spin_lock_offset[id], cdp.spin_lock_nu1[id]
print ""
cdp.temp = []
for exp_type, frq, offset, point, ei, mi, oi, di in
loop_exp_frq_offset_point(return_indices=True):
for time, ti in loop_time(exp_type=exp_type, frq=frq,
offset=offset, point=point, return_indices=True):
print exp_type, frq, offset, point, time
cdp.temp.append([exp_type, frq, offset, point, time])
------2_pre_run_r2eff.py
# Python module imports.
from os import sep, getcwd
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
# Analysis variables.
#####################
# The dispersion models.
MODELS = ['R2eff']
# The grid search size (the number of increments per dimension).
GRID_INC = 11
# The number of Monte Carlo simulations to be used for error analysis
at the end of the analysis.
MC_NUM = 10
# A flag which if True will activate Monte Carlo simulations for all
models. Note this will hugely increase the computation time.
MC_SIM_ALL_MODELS = False
# The results directory.
RESULTS_DIR = getcwd() + sep + 'results_T'
# The directory of results of an earlier analysis without clustering.
PRE_RUN_DIR = None
# The model selection technique to use.
MODSEL = 'AIC'
# The flag for only using numeric models in the final model selection.
NUMERIC_ONLY = False
# The R1rho value in rad/s by which to judge insignificance. If the
maximum difference between two points on all dispersion curves for a
spin is less than this value, that spin will be deselected.
INSIGNIFICANCE = 1.0
# Run the setup script
script('1_setup_r1rho.py')
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
# Auto-analysis execution.
##########################
# Do not change!
Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=RESULTS_DIR, models=MODELS, grid_inc=GRID_INC,
mc_sim_num=MC_NUM, modsel=MODSEL, insignificance=INSIGNIFICANCE,
numeric_only=NUMERIC_ONLY)
2014-08-22 23:01 GMT+02:00 Atul Srivastava <asriv...@umn.edu>:
> Dear Edward,
>
> Thanks for providing help and insights. I used an improved script. The
> scripts is able to calculate the R2eff and the omegaeffective properly, but
> it is not able to fit any model. It also sees dispersion point as a constant
> 1500 Hz (see attached file in results/R2eff/disp_55_N.out).
>
> I have attached all sample data, script and results for your review. Please
> see the last few lines in the log file for the error message.
>
> Thanks,
> Atul
>
>
>
>
> On Fri, Aug 22, 2014 at 3:02 AM, Edward d'Auvergne <edw...@nmr-relax.com>
> wrote:
>>
>> Hi Atul,
>>
>> Again continuing from Troels' post at
>> http://thread.gmane.org/gmane.science.nmr.relax.user/1718/focus=1732.
>> Well, actually, as Troels fully covered all of you questions in more
>> detail than I could have provided, I don't have anything to add. If
>> you have other questions, please don't hesitate to ask.
>>
>> Regards,
>>
>> Edward
>>
>>
>> On 21 August 2014 12:00, Troels Emtekær Linnet <tlin...@nmr-relax.com>
>> wrote:
>>
>> [snip]
>>
>> > relax_disp.relax_time(spectrum_id=id, time=relax_time)
>> > -> This is used for the initial R2eff calculation, for exponential
>> > curve fitting.
>> >
>> > # Set the NMR field strength of the spectrum.
>> > spectrometer.frequency(id=id, frq=H_frq)
>> > -> This is used for conversion between nucleus, etc.
>> >
>> > # Load the R1 data.
>> > relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6,
>> > file='R1_500MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2,
>> > res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6,
>> > error_col=7)
>> > -> R1 needs to be loaded. This is because that R1 is part of the
>> > equations. :-) The next release of relax, will implement feature where
>> > R1 is fitted.
>> >> Note, that fitting introduces another variable in the equations.
>> >
>> > # Read the chemical shift data.
>> > chemical_shift.read(file='ref_500MHz.list', dir=DATA_PATH)
>> >
>> > -> This is needed to get the ppm position of the nucleus.
>> > -> See now:
>> > http://www.nmr-relax.com/manual/Dispersion_model_summary.html
>> > -> The "average resonance in the rotating frame" Omega(bar) = w_(bar) -
>> > w_rf."
>> > -> Here w_bar is the chemical shift, and w_rf is the offset.
>> > -> Let is review figure Fig1_Palmer_Massi_2006.png
>> > -> This is the S_z axis.
>> >
>> > That should be it.
>> >
>> > If you have any questions, please don't hesitate to write again.
>> >
>> > If you need more help, consider writing a support request on the
>> > homepage tracker.
>> > - https://gna.org/support/?group=relax
>> >
>> > Add following information:
>> > # Please attach a system info file
>> >> relax -i -t relax_i.txt
>> >
>> > # Please write up, which buttons you pushed, or attach your script.
>> > # Consider adding your data in "sample" format. Meaning that you
>> > delete all confidential information from the files, and only have 1-2
>> > residues left for testing.
>> >
>> > If you write such a support request, it it easier to share script files,
>> > and
>> > help other users.
>> >
>> > The benefits from such a support request is:
>> > - The information is available to all users, which can benefit
>> > others in same situation.
>> > - The information can be tracked back.
>> > - The relax manual can be expanded, to help future users in same
>> > situation.
>> >
>> >
>> > Good luck!
>> >
>> > Best
>> > Troels Emtekær Linnet
>> > PhD student
>> > Copenhagen University
>> > SBiNLab, 3-0-41
>> > Ole Maaloes Vej 5
>> > 2200 Copenhagen N
>> > Tlf: +45 353-22083
>> > Lync Tlf: +45 353-30195
>
>
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-users mailing list
relax-users@gna.org
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
