Ah ja. :-)
I found the information in:
specific_analyses/relax_disp/api.py
specific_analyses/relax_disp/disp_data.py
It is the return_offset_data() function.
For reference:
----------------
# Convert the shift from ppm to rad/s and store it.
shifts[spin_index, frq_index] = spin.chemical_shift * 2.0 * pi * frq / g1H
* return_gyromagnetic_ratio(spin.isotope) * 1e-6
# Store the offset in rad/s.
offsets[spin_index, frq_index, disp_pt_index] = cdp.spin_lock_offset[id] *
2.0 * pi * frq / g1H * return_gyromagnetic_ratio(spin.isotope) * 1e-6
# Calculate the tilt angle.
point = cdp.spin_lock_nu1[id]
omega1 = point * 2.0 * pi
Delta_omega = shifts[spin_index, frq_index] - offsets[spin_index,
frq_index, disp_pt_index]
if Delta_omega == 0.0:
theta[spin_index, frq_index, disp_pt_index] = pi / 2.0
else:
theta[spin_index, frq_index, disp_pt_index] = atan(omega1 / Delta_omega)
------------------
Which resembles:
$OMEGA=($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));
2013/10/22 Edward d'Auvergne <[email protected]>
> 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
> >> >> >> >
> >> >> >
> >> >> >
> >> >
> >> >
> >
> >
>
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