Re: Help with settings script for R1rho analysis. -- October 22, 2013 - 14:55

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
>> >
>> > 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
>> >
>
>