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
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> >> >> >
> >> >
> >> >
> >
> >
>
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