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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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