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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