I have to give up for the day, but just a quick hint - look in the modules of the specific_analyses.relax_disp package! The disp_data module is probably your best bet.
Bye, Edward On 22 October 2013 19:16, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > I prefer to do the calculations straight away in my scripts, from the > information which is ex-tractable from the procpar files. > But I guess that is a matter of taste. > > But now I think I got it. :-) Thanks! > I guess that relax calculates "omega_rf_ppm - chemShift{peakName} ", but I > could not locate this functions call. > ( I do load the chemical shifts from a SPARKY list, (the seriesTab format is > not yet supported). ) > > > I now do the settings script, by settting variables: > # In MHz > yOBS = 81.050 > # In ppm > yCAR = 118.078 > centerPPM_N15 = yCAR > > And then I calculate the offset in ppm for each spectrum. > > # Calculating the spin-lock offset in ppm, from offsets values provided in > Hz. > #frq_N15_Hz = set_sfrq * 1E6 * gyro15N / gyro1H > frq_N15_Hz = yOBS * 1E6 > offset_ppm_N15 = float(deltadof2) / frq_N15_Hz * 1E6 > omega_rf_ppm = centerPPM_N15 + offset_ppm_N15 > > And the range is now 118.078 ppm to 241.45 ppm. > > I tried to locate the corresponding calculation of OMEGA in relax, but i was > not successful. > I looked in: > > lib/dispersion/dpl94.py > target_functions/relax_disp.py > > I wonder where how to locate the calculation of theta? > > Best > Troels > > > > > > > 2013/10/22 Edward d'Auvergne <[email protected]> >> >> Hi, >> >> You could look at the relax code for how omega_eff is calculated. >> However you will never use this - it is never input into relax. If >> you have a look at the sample_scripts/relax_disp/R1rho_analysis.py >> script, you will see that all is needed is an equivalent of the table: >> >> # The spectral data - spectrum ID, peak list file name, spin-lock >> field strength (Hz), the spin-lock offset (ppm), the relaxation time >> (s), spectrometer frequency (Hz), and experimental error (RMSD of the >> base plane noise for each spectrum). >> data = [ >> ['ref_500MHz', 'ref_500MHz.list', , None, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_1000.0_500MHz', 'nu_1000.0_500MHz.list', 1000.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_1500.0_500MHz', 'nu_1500.0_500MHz.list', 1500.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_2000.0_500MHz', 'nu_2000.0_500MHz.list', 2000.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_2500.0_500MHz', 'nu_2500.0_500MHz.list', 2500.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_3000.0_500MHz', 'nu_3000.0_500MHz.list', 3000.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_3500.0_500MHz', 'nu_3500.0_500MHz.list', 3500.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_4000.0_500MHz', 'nu_4000.0_500MHz.list', 4000.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_4500.0_500MHz', 'nu_4500.0_500MHz.list', 4500.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_5000.0_500MHz', 'nu_5000.0_500MHz.list', 5000.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_5500.0_500MHz', 'nu_5500.0_500MHz.list', 5500.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['nu_6000.0_500MHz', 'nu_6000.0_500MHz.list', 6000.0, 110.0, 0.1, >> 500e6, 200000.0] >> ['ref_800MHz', 'ref_800MHz.list', , None, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_1000.0_800MHz', 'nu_1000.0_800MHz.list', 1000.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_1500.0_800MHz', 'nu_1500.0_800MHz.list', 1500.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_2000.0_800MHz', 'nu_2000.0_800MHz.list', 2000.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_2500.0_800MHz', 'nu_2500.0_800MHz.list', 2500.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_3000.0_800MHz', 'nu_3000.0_800MHz.list', 3000.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_3500.0_800MHz', 'nu_3500.0_800MHz.list', 3500.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_4000.0_800MHz', 'nu_4000.0_800MHz.list', 4000.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_4500.0_800MHz', 'nu_4500.0_800MHz.list', 4500.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_5000.0_800MHz', 'nu_5000.0_800MHz.list', 5000.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_5500.0_800MHz', 'nu_5500.0_800MHz.list', 5500.0, 110.0, 0.1, >> 800e6, 200000.0] >> ['nu_6000.0_800MHz', 'nu_6000.0_800MHz.list', 6000.0, 110.0, 0.1, >> 800e6, 200000.0] >> ] >> >> These values can be hardcoded into a script. There is no need to do >> this programatically - they will not change. Though you could >> programmatically generate such a table in a separate script, if you >> wish. You almost have this table anyway with the >> exp_parameters_sort.txt file. It is good, for sanity's sake, to have >> such a complete summary table in the standard units. As for >> omega_eff, it uses the data in this table together with the chemical >> shifts loaded via the chemical_shift.read user function to >> automatically determine the values. It would be best read these >> shifts from one of your *.ser files. >> >> I would recommend to use the >> sample_scripts/relax_disp/R1rho_analysis.py script as a template for >> your whole analysis. For the test suite, I would recommend copying >> test_suite/system_tests/scripts/relax_disp/r1rho_off_res_tp02.py and >> making a few minor modifications. For example using a table as in the >> sample script. This r1rho_off_res_tp02.py script does not have a >> table as it deals with perfect synthetic data. >> >> Regards, >> >> Edward >> >> On 22 October 2013 14:54, Troels Emtekær Linnet <[email protected]> >> wrote: >> > Hi Edward. >> > >> > I am digging through old perl scripts, which is preparing data for our >> > analysis in IgorPro. >> > >> > So I guess my challenge is now to match this to the procedures of relax, >> > and >> > establish the difference. >> > >> > ----------- >> > $expList="expList.txt"; >> > $peakFile='peaks.dat'; >> > $centerPPM=118.085; >> > $frq=81.050; >> > ----------- >> > >> > expList.txt contains lines with: "fit_R1_filename" >> > "spin_lock_offset_HZ" >> > "spin_lock_field_Hz" >> > >> > ---------------------- >> > open IN, "$expList" or die "Cannot open $expList for read"; >> > while (<IN>){ >> > @process = split (/\s+/, $_); >> > if ($process[0] ne "#"){ >> > $fileName{$i}=$process[0]; >> > $offset{$i}=$process[1]; >> > $omega1{$i}=$process[2]; >> > $i++; >> > }; >> > }; >> > close (IN); >> > ------------------- >> > >> > And then it read the peak file to extract ppm for N15. >> > >> > ------------- >> > open IN , "$peakFile" or die "Cannot open $peakFile for read"; >> > while (<IN>) { >> > @process = split (/\s+/, $_); >> > if ($process[0] eq ""){splice (@process, 0, 1)}; >> > if ($process[0] == 1){ $read = 1}; >> > if ($read == 1){ >> > $chemShift{$process[6]}=$process[4]; >> > }; >> > }; >> > close (IN); >> > ----------- >> > The chemical shifts are stored in a dictionary under the residue name >> > ($process[6]) with the ppm values of N15 ($process[4]). >> > >> > Then R1r and R1r_err are read in from external exponential fit files. >> > ------------ >> > for ($i = 1; $i <= $numFiles; $i++){ >> > open IN, "$fileName{$i}" or die "Cannot open $fileName{$i} for read"; >> > while (<IN>){ >> > @process = split (/\s+/, $_); >> > if ($process[0] ne "#"){ >> > $R1r{$process[0]}{$i}=$process[1]; >> > $R1r_err{$process[0]}{$i}=$process[2]; >> > }; >> > }; >> > close(IN); >> > }; >> > ------------------- >> > >> > >> > Then omega is calculated. >> > ------------ >> > foreach $peakName (keys %chemShift) { >> > open (OUT, ">../residueFiles/$peakName.dat"); >> > for ($i=1;$i<=$numFiles;$i++){ >> > $OMEGA=($centerPPM-$chemShift{$peakName})*$frq+$offset{$i}; >> > $omegaEFF=sqrt($OMEGA**2+$omega1{$i}**2); >> > if (($omega1{$i}/$OMEGA) > 0){ >> > $theta=180/$PI*abs(atan($omega1{$i}/$OMEGA)); >> > }else{ >> > $theta=180-180/$PI*abs(atan($omega1{$i}/$OMEGA)); >> > }; >> > printf OUT "%s %s %s %s %s >> > >> > %s\n",$OMEGA,$omega1{$i},$omegaEFF,$theta,$R1r{$peakName}{$i},$R1r_err{$peakName}{$i}; >> > }; >> > close (OUT); >> > }; >> > -------------- >> > >> > I guess I would need to find out how relax calculates omegaEFF, the >> > effective field in the rotating frame ? >> > >> > Best >> > Troels >> > >> > >> > >> > >> > 2013/10/22 Edward d'Auvergne <[email protected]> >> >> >> >> Hi, >> >> >> >> Ok, I made the assumption that deltadof2 was not the spin-lock offset >> >> (in ppm) but rather the spin-lock field strength (in Hz). The ppm >> >> values as printed out from the r1rho_1_ini.py script are far too low >> >> for 15N. They should be in the range of 100-120 ppm! I.e. around the >> >> 15N chemical shifts. They can be much higher and much lower for >> >> off-resonance data, but having many at an offset of 0.0 ppm seems a >> >> little strange. >> >> >> >> Regards, >> >> >> >> Edward >> >> >> >> On 22 October 2013 13:18, Troels Emtekær Linnet <[email protected]> >> >> wrote: >> >> > Hi Edward. >> >> > >> >> > Thanks for looking at this. >> >> > >> >> > The offset for N15 spinlock is given in Hz as parameter deltadof2 >> >> > for our pulse sequence. >> >> > >> >> > So I guess that this conversions should be appropriate: >> >> > omega_rf_ppm = float(deltadof2) / (set_sfrq * 1E6) * 1E6 >> >> > >> >> > where set_sfrq=799.7773991 is the spectrometer frequency. >> >> > >> >> > Best >> >> > Troels >> >> > >> >> > >> >> > 2013/10/22 Edward d'Auvergne <[email protected]> >> >> >> >> >> >> Hi, >> >> >> >> >> >> In the relax prompt, have a look at: >> >> >> >> >> >> relax> help(relax_disp.spin_lock_offset) >> >> >> >> >> >> The unit you need is ppm. You can find this number directly from >> >> >> the >> >> >> Bruker acqus or Varian procpar files. It is the ppm offset of the >> >> >> spin-lock pulse which is manually set by the person recording for >> >> >> each >> >> >> spectrum. You may need to go to the original pulse sequence to know >> >> >> which pulse this is. It will be a fixed value for each spectrum >> >> >> collected and you can use that value directly. The calculations in >> >> >> your scripts seem far to complicated and it looks like the internal >> >> >> conversions performed within relax. You should never need >> >> >> gyromagnetic ratios, factors of pi, etc. If you do, you should >> >> >> probably go back to the original experiments and pull out the >> >> >> correct >> >> >> offset number in ppm for each spectrum. I hope this helps. >> >> >> >> >> >> Regards, >> >> >> >> >> >> Edward >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On 22 October 2013 10:46, Troels Emtekær Linnet >> >> >> <[email protected]> >> >> >> wrote: >> >> >> > Hi Edward. >> >> >> > >> >> >> > I wonder if would have time to look at the settings script in: >> >> >> > test_suite/shared_data/dispersion/Kjaergaard_et_al_2013 >> >> >> > >> >> >> > It is the scripts: >> >> >> > r1rho_1_ini.py >> >> >> > r1rho_3_spectra_settings.py >> >> >> > >> >> >> > In r1rho, I am unsure if I do the correct conversion from Hz to >> >> >> > ppm >> >> >> > for >> >> >> > omega_rf. >> >> >> > >> >> >> > Again, if there is hidden radian units? >> >> >> > >> >> >> > It is when I set: >> >> >> > relax_disp.spin_lock_offset >> >> >> > >> >> >> > And I wonder, how to start modifying, so R1 rates can be read per >> >> >> > spectra? >> >> >> > >> >> >> > Best >> >> >> > Troels >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > _______________________________________________ >> >> >> > relax (http://www.nmr-relax.com) >> >> >> > >> >> >> > This is the relax-devel mailing list >> >> >> > [email protected] >> >> >> > >> >> >> > 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-devel >> >> >> > >> >> > >> >> > >> > >> > > > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] 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-devel
