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 > >>> > >>> 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 > _______________________________________________ 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
