Re: Help with settings script for R1rho analysis.Re: Help with settings script for R1rho analysis.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 <tlinnet@xxxxxxxxxxxxx> 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 <edward@xxxxxxxxxxxxx>
>>
>> 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 <tlinnet@xxxxxxxxxxxxx>
>> 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 <edward@xxxxxxxxxxxxx>
>> >>
>> >> 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 <tlinnet@xxxxxxxxxxxxx>
>> >> 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 <edward@xxxxxxxxxxxxx>
>> >> >>
>> >> >> 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
>> >> >> <tlinnet@xxxxxxxxxxxxx>
>> >> >> 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
>> >> >> > relax-devel@xxxxxxx
>> >> >> >
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>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>