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 >> >> 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 _______________________________________________ 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
