field strength off-resonance R1rho constant relax time relaxation dispersion
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, 9], ['900MHz_2100.list','2100_off_reso_R1rho_ubi_2.list', 2100, 118.275, 0.320, 900.21422558574e6, 9], ['900MHz_2728.list','2728_off_reso_R1rho_ubi_3.list', 2728, 118.275, 0.320, 900.21422558574e6, 9], ['900MHz_3357.list','3357_reso_R1rho_ubi_4.list', 3357, 118.275, 0.320, 900.21422558574e6, 9], ['900MHz_3985.list','3985_off_reso_R1rho_ubi_5.list', 3985, 118.275, 0.320, 900.21422558574e6, 9], ['900MHz_4614.list','4614_off_reso_R1rho_ubi_6.list', 4614, 118.275, 0.320, 900.21422558574e6, 9], ['900MHz_rep_4614.list','4614_rep_off_reso_R1rho_ubi_10.list', 4614, 118.275, 0.320, 900.21422558574e6, 9], ['900MHz_5242.list','5242_off_reso_R1rho_ubi_7.list', 5242, 118.275, 0.320, 900.21422558574e6, 9], ['900MHz_5871.list','5871_off_reso_R1rho_ubi_8.list', 5871, 118.275, 0.320, 900.21422558574e6, 9], ['900MHz_6500.list','6500_off_reso_R1rho_ubi_9.list', 6500, 118.275, 0.320, 900.21422558574e6, 9] ] # 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
Re: field strength off-resonance R1rho constant relax time relaxation dispersion
oking 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 :
> >>> 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, 9],
> >>> ['900MHz_2100.list','2100_off_reso_R1rho_ubi_2.list',
> 2100,
> >>> 118.275, 0.320, 900.21422558574e6, 9],
> >>> ['900MHz_2728.list','2728_off_reso_R1rho_ubi_3.list',
> 2728,
> >>> 118.275, 0.320, 900.21422558574e6, 9],
> >>> ['900MHz_3357.list','3357_reso_R1rho_ubi_4.list',
> 3357,
> >>> 118.275, 0.320, 900.21422558574e6, 9],
> >>> ['900MHz_3985.list','3985_off_reso_R1rho_ubi_5.list',
> 3985,
> >>> 118.275
Re: field strength off-resonance R1rho constant relax time relaxation dispersion
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, 9], ['900MHz_2100','2100_off_reso_R1rho_ubi_2.list', 2100, 1500, 0.320, 900.0e6, 9], ['900MHz_2728','2728_off_reso_R1rho_ubi_3.list', 2728, 1500, 0.320, 900.0e6, 9], ['900MHz_3357','3357_reso_R1rho_ubi_4.list', 3357, 1500, 0.320, 900.0e6, 9], ['900MHz_3985','3985_off_reso_R1rho_ubi_5.list', 3985, 1500, 0.320, 900.0e6, 9], ['900MHz_4614','4614_off_reso_R1rho_ubi_6.list', 4614, 1500, 0.320, 900.0e6, 9], ['900MHz_rep_4614','4614_rep_off_reso_R1rho_ubi_10.list', 4614, 1500, 0.320, 900.0e6, 9], ['900MHz_5242','5242_off_reso_R1rho_ubi_7.list', 5242, 1500, 0.320, 900.0e6, 9], ['900MHz_5871','5871_off_reso_R1rho_ubi_8.list', 5871, 1500, 0.320, 900.0e6, 9], ['900MHz_6500','6500_off_reso_R1rho_ubi_9.list', 6500, 1500, 0.320, 900.0e6, 9] ] --- 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 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 > 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 >> 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
Re: field strength off-resonance R1rho constant relax time relaxation dispersion
Dear Edward, Thanks for providing help and insights. I used an improved script. The scripts is able to calculate the R2eff and the omegaeffective properly, but it is not able to fit any model. It also sees dispersion point as a constant 1500 Hz (see attached file in results/R2eff/disp_55_N.out). I have attached all sample data, script and results for your review. Please see the last few lines in the log file for the error message. Thanks, Atul On Fri, Aug 22, 2014 at 3:02 AM, Edward d'Auvergne wrote: > Hi Atul, > > Again continuing from Troels' post at > http://thread.gmane.org/gmane.science.nmr.relax.user/1718/focus=1732. > Well, actually, as Troels fully covered all of you questions in more > detail than I could have provided, I don't have anything to add. If > you have other questions, please don't hesitate to ask. > > Regards, > > Edward > > > On 21 August 2014 12:00, Troels Emtekær Linnet > wrote: > > [snip] > > > relax_disp.relax_time(spectrum_id=id, time=relax_time) > > -> This is used for the initial R2eff calculation, for exponential > > curve fitting. > > > > # Set the NMR field strength of the spectrum. > > spectrometer.frequency(id=id, frq=H_frq) > > -> This is used for conversion between nucleus, etc. > > > > # Load the R1 data. > > relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6, > > file='R1_500MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2, > > res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, > > error_col=7) > > -> R1 needs to be loaded. This is because that R1 is part of the > > equations. :-) The next release of relax, will implement feature where > > R1 is fitted. > >> Note, that fitting introduces another variable in the equations. > > > > # Read the chemical shift data. > > chemical_shift.read(file='ref_500MHz.list', dir=DATA_PATH) > > > > -> This is needed to get the ppm position of the nucleus. > > -> See now: > http://www.nmr-relax.com/manual/Dispersion_model_summary.html > > -> The "average resonance in the rotating frame" Omega(bar) = w_(bar) - > w_rf." > > -> Here w_bar is the chemical shift, and w_rf is the offset. > > -> Let is review figure Fig1_Palmer_Massi_2006.png > > -> This is the S_z axis. > > > > That should be it. > > > > If you have any questions, please don't hesitate to write again. > > > > If you need more help, consider writing a support request on the > > homepage tracker. > > - https://gna.org/support/?group=relax > > > > Add following information: > > # Please attach a system info file > >> relax -i -t relax_i.txt > > > > # Please write up, which buttons you pushed, or attach your script. > > # Consider adding your data in "sample" format. Meaning that you > > delete all confidential information from the files, and only have 1-2 > > residues left for testing. > > > > If you write such a support request, it it easier to share script files, > and > > help other users. > > > > The benefits from such a support request is: > > - The information is available to all users, which can benefit > > others in same situation. > > - The information can be tracked back. > > - The relax manual can be expanded, to help future users in same > situation. > > > > > > 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 > ___ 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
