Dear Edward,
I already mentioned the issue but I realized that perhaps the question was
not very clear.
Following is the situation I am trying to solve by 'relax':
I have constant-relaxation-time relaxation-dispersion data for
off-resonance 15N R1rho acquired on Bruker spectrometers (I would like to
mention that I have 15N R1 data as well) at two magnetic fields.
In this relaxation-dispersion experiment I have used a constant spin-lock
amplitude of 1500 Hz. Spin-lock time was 0.04 second.
I varied only the position of the spin-lock carrier. The distance (in Hz)
between the center of the spectrum (along 15N dimension) and the spin-lock
carrier were 2100, 2728, ... .... ... ...6500 Hz.
As you know that the effective field sensed by each spin will be different
according to the position of the peak in the spectrum. I tried to calculate
that by 'relax' that gave a output file 'w2_eff.out'; but these values did
not match with what I calculated manually.
I request you to please provide a new sample script for the
relaxation-dispersion analysis appropriate for the above mentioned case.
Further, in the following format the column for offset (third column) does
not accept 'None' which I needed to set reference intensity. It returns the
message "RelaxError: The offset value must be provided.". However, the
program accepts 'None' for 'field',.
--------------------------------------------------------------------------------------------------------------------------------------------------
data = [
['900MHz_reference', 'ref_off_reso_R1rho_ubi_1.list', None, 1500,
0.320, 900.0e6, 90000],
['900MHz_2100', '2100_off_reso_R1rho_ubi_2.list', 2100, 1500,
0.320, 900.0e6, 90000],
['900MHz_2728', '2728_off_reso_R1rho_ubi_3.list', 2728, 1500,
0.320, 900.0e6, 90000],
['900MHz_3357', '3357_reso_R1rho_ubi_4.list', 3357, 1500,
0.320, 900.0e6, 90000],
['900MHz_3985', '3985_off_reso_R1rho_ubi_5.list', 3985, 1500,
0.320, 900.0e6, 90000],
['900MHz_4614', '4614_off_reso_R1rho_ubi_6.list', 4614, 1500,
0.320, 900.0e6, 90000],
['900MHz_rep_4614','4614_rep_off_reso_R1rho_ubi_10.list', 4614, 1500,
0.320, 900.0e6, 90000],
['900MHz_5242', '5242_off_reso_R1rho_ubi_7.list', 5242, 1500,
0.320, 900.0e6, 90000],
['900MHz_5871', '5871_off_reso_R1rho_ubi_8.list', 5871, 1500,
0.320, 900.0e6, 90000],
['900MHz_6500', '6500_off_reso_R1rho_ubi_9.list', 6500, 1500,
0.320, 900.0e6, 90000]
]
---------------------------------------------------------------------------------------------------------------------------------------------------
I emphasized few things above for clarity, though they are trivial for you.
Thanks,
Atul
On Tue, Aug 19, 2014 at 9:52 AM, Atul Srivastava <asriv...@umn.edu> wrote:
> Hi Edward,
>
> Thanks for yours and Troels' kind help. I am trying to get the data on
> second field.
> I am still working with the test data and trying to analyze few residues
> manually to check if the analysis is consistent. I will update you once I
> am satisfied with my analysis.
>
> Thanks again,
> Atul
>
>
> On Mon, Aug 18, 2014 at 2:37 AM, Edward d'Auvergne <edw...@nmr-relax.com>
> wrote:
>
>> 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 <tlin...@nmr-relax.com>
>> 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 <tlin...@nmr-relax.com
>> >:
>> >> 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 <asriv...@umn.edu>:
>> >>> 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
>> >>> _______________________________________________
>> >>> relax (http://www.nmr-relax.com)
>> >>>
>> >>> This is the relax-users mailing list
>> >>> relax-users@gna.org
>> >>>
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>> >>> reminder, or change your subscription options,
>> >>> visit the list information page at
>> >>> https://mail.gna.org/listinfo/relax-users
>> >
>> > _______________________________________________
>> > relax (http://www.nmr-relax.com)
>> >
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>
>
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