Hi Atul,
I have just returned from holidays, hence my late reply. However
Troels' reply should have fully addressed your questions and issues.
Is the analysis now working for you? Note that the spin-lock
amplitude Omega_1 is the spin-lock field strength or nu_1, as you have
supplied (converted using the factor of 2*pi). Tilt angles and
anything else the specific model requires are calculated from this and
the difference of the spin's chemical shift and the experiment
specific spin-lock offset.
Regards,
Edward
On 2 August 2014 09:52, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>
wrote:
Dear Atul.
I forgot one question.
Do you have R1 data available?
relax cannot currently do calculation without these measured values.
relax_data.read(ri_id='R1', ri_type='R1',
frq=cdp.spectrometer_frq_list[0], file= .....)
I am about to try to also make it possible to fit R1 values.
sr #3135: Optimisation of the R1 relaxation rate for the off-resonance
R1rho relaxation dispersion models.
https://gna.org/support/?3135
But that can take some weeks before it is implemented, and tested
properly.
Best
Troels
2014-08-02 9:47 GMT+02:00 Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>:
Dear Atul.
Welcome to the mailing list!
This question is a very good one, and is not covered good enough in the
manual !
There has been a question related to this question on the mailing list
recently.
From Peixiang, at:
http://thread.gmane.org/gmane.science.nmr.relax.user/1654
http://thread.gmane.org/gmane.science.nmr.relax.user/1666
http://thread.gmane.org/gmane.science.nmr.relax.user/1667
Try to go through these post first, to cover the background.
Don't get to confused, I will give you the answer below. :-)
By asking here on the public mailing list, your question will
potentially help any other users who would
have the same question. And it will help us to turn our attention to
the manual lacking a tutorial for R1rho models.
For example this mailing list can be viewed here:
http://thread.gmane.org/gmane.science.nmr.relax.user
And searches in same mail directory can be done here:
http://dir.gmane.org/gmane.science.nmr.relax.user
Your specific question is now listed here:
http://thread.gmane.org/gmane.science.nmr.relax.user/1718
Edward can probably extend the your answer into details.
I know, that he is on holiday for the next two weeks, so I can try to
answer your question.
I am a PhD student at the structural biology in Copenhagen, and have
been working on the dispersion branch (CPMG and R1rho).
So I will however do my best to try to help you in the meantime.
##### How to get help
How to find help:
The manual
http://wiki.nmr-relax.com/Manual
Related to: Relaxation Dispersion:
http://www.nmr-relax.com/manual/Relaxation_dispersion.html
http://www.nmr-relax.com/manual/Relaxation_dispersion_optimisation_theory.html
http://www.nmr-relax.com/manual/Analysing_dispersion_in_prompt_script_UI_mode.html
http://www.nmr-relax.com/manual/Dispersion_model_summary.html
It seems we have a problem, that setting up R1rho experiments is not
covered in well the manual.
Then I see that you have found the folder with sample scripts.
The sample script at:
cat sample_scripts/relax_disp/R1rho_analysis.py
Did you know, that you can get help to all the functions?
You can start relax, and see the help information this way:
relax
help(sequence.read)
help(spectrum.read_intensities)
But what you are looking for is this:
help(relax_disp.spin_lock_field)
help(relax_disp.spin_lock_offset)
Or go to the GUI, and in the top select:
user functions (n-z) -> relax_disp -> spin_lock_field
---------
Relax has something called "system tests", which make sure that all
functions of relax is kept when changing the code.
Try opening the setup of one of these systemtests:
gedit test_suite/system_tests/relax_disp.py
And search for "def setup_r1rho_kjaergaard".
Skip all lines with:
- self.assertEqual
Delete all:
- self.interpreter
Here you can get another way to inspire you how to setup things.
Test data resides in:
cd test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/
And have been analysed by:
http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_r1rho_fixed_time_recorded_on_varian_as_sequential_spectra#Intro
So back to your question.
You mention spin-lock amplitude.
This is in relax called "spin-lock field" or " spin-lock field
strength".
If we set in the setup:
-----
# In MHz.
yOBS = 81.050
# In ppm
yCAR = 118.078
centerPPM_N15 = yCAR
-------
# So for varian giving offset in Hertz, and relax wants in ppm:
# Calculating the spin-lock offset in ppm, from offsets values provided
in Hz.
frq_N15_Hz = yOBS * 1E6
offset_ppm_N15 = float(deltadof2) / frq_N15_Hz * 1E6
omega_rf_ppm = centerPPM_N15 + offset_ppm_N15
# Set The spin-lock offset, omega_rf, in ppm.
relax_disp.spin_lock_offset(spectrum_id=sp_id, offset=omega_rf_ppm)
For this experiment, we first had to do a calibration experiment to
find how the lock power translated into field strength.
That results is written into a python dictionary in the setup:
spin_lock_field_strengths_Hz = {'35': 431.0, '39': 651.2, '41': 800.5,
'43': 984.0, '46': 1341.11, '48': 1648.5}
# Looping over file with all settings:
dpwr2slock = line.split()[3]
spin_lock_field_strength = spin_lock_field_strengths_Hz[dpwr2slock]
# Set The spin-lock field strength, nu1, in Hz
relax_disp.spin_lock_field(spectrum_id=sp_id,
field=spin_lock_field_strength)
I hope this helps!
Please write back here to the mailing list, if the answer covers your
question.
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
2014-08-01 19:42 GMT+02:00 Atul Srivastava <asrivast@xxxxxxx>:
Dear Edward,
I am trying to use 'relax' for the off-resonance R1rho
constant-relaxation-time relaxation dispersion using R1rho_analysis.py
script available as sample script with relax.
The following is the section where I have question:
---------------------------------------------------------------------------------------
data = [
['900MHz_reference_3000.list', 'ref_off_reso_R1rho_ubi_1.list',
None, 118.275, 0.320, 900.21422558574e6, 90000],
['900MHz_2100.list', '2100_off_reso_R1rho_ubi_2.list',
2100,
118.275, 0.320, 900.21422558574e6, 90000],
['900MHz_2728.list', '2728_off_reso_R1rho_ubi_3.list',
2728,
118.275, 0.320, 900.21422558574e6, 90000],
['900MHz_3357.list', '3357_reso_R1rho_ubi_4.list',
3357,
118.275, 0.320, 900.21422558574e6, 90000],
['900MHz_3985.list', '3985_off_reso_R1rho_ubi_5.list',
3985,
118.275, 0.320, 900.21422558574e6, 90000],
['900MHz_4614.list', '4614_off_reso_R1rho_ubi_6.list',
4614,
118.275, 0.320, 900.21422558574e6, 90000],
['900MHz_rep_4614.list','4614_rep_off_reso_R1rho_ubi_10.list',
4614,
118.275, 0.320, 900.21422558574e6, 90000],
['900MHz_5242.list', '5242_off_reso_R1rho_ubi_7.list',
5242,
118.275, 0.320, 900.21422558574e6, 90000],
['900MHz_5871.list', '5871_off_reso_R1rho_ubi_8.list',
5871,
118.275, 0.320, 900.21422558574e6, 90000],
['900MHz_6500.list', '6500_off_reso_R1rho_ubi_9.list',
6500,
118.275, 0.320, 900.21422558574e6, 90000]
]
# Loop over the spectra.
for id, file, field, offset, relax_time, H_frq, rmsd in data:
# 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)
------------------------------------------------------------------------------------------------------
I have supplied the spin lock offset from the center of the spectrum
in Hz
for "field".
And the center of spectrum in ppm as 118.275 ppm for "offset".
However, I wonder where the value of spin-lock amplitude is to be
provided
as it is indispensable for the calculation of spin-lock effective
field. I
have acquired my data with spinlock amplitude 1500 kz with different
offset
values for 15N spin.
Please let me know that at your earliest convenience.
Thanks for your time and consideration.
Sincerely,
Atul
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_______________________________________________
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Re: field strength off-resonance R1rho constant relax time relaxation dispersion