PRESS (Magnetic Resonance Spectroscopy)

****** The System *******
spectrometer(MHz)  168.22
spinning_freq(kHz) *
channels           H1
nuclei             H1 H1 H1 H1 H1 H1 H1
atomic_coords      *
cs_isotropic       myo-inositol.cs ppm
csa_parameters     *
j_coupling         myo-inositol.j
quadrupole         *
dip_switchboard    *
csa_switchboard    *
exchange_nuclei    *
bond_len_nuclei    *
bond_ang_nuclei    *
tors_ang_nuclei    *
groups_nuclei      *
******* Pulse Sequence *********************************************************************
CHN 1
timing(usec)      (t128.tm) 1 (5000) 1 (0) (t200.tm) (0) 1 (30000) 1 (t200.tm) 1 (25000) (500)8192
power(kHz)         e.pwr    0   0    0  0   a.pwr     0  0   0     0   a.pwr   0   0      0
phase(deg)          90      0   0    0  0     0       0  0   0     0     0     0   0      0
freq_offs(kHz)       0      0   0    0  0     0       0  0   0     0     0     0   0      0
******* Variables **************************************************************************

*** Comments on the pulse sequence:
* e.pwr and a.pwr are the selective excitation and refocusing shaped pulses, respectively; (5000) (30000) and (25000) are the delays; (0) pulses are used two select coherences; 1-usec pulses are the crusher gradients
* the pulse sequence is set up to perform the simulation of PRESS in two different ways:
* 1) via explicit coherence selection (using the two (0) pulses above)
* 2) via averaging over the phases created by the crusher gradients
* The first way is more efficient and rigorously correct theoretically; the second way may suffer (at least in principle) from the effects of residual high-order coherences
*********************************************************************************************

* set the step sizes of the shaped pulses
pulse_1_[1 6 11]=[20 25 25]
* convert mT to kHz: 42.5773kHz/mT
psf_1_[1 6 11]=42.5773
* see comments below
ppm_ref_offs_1=0.16822*3.5
** localization point **
frs_1_[1 6 11]=[0.5 0 0.5]

* remove the freq.-offset-dependent phase created by the selective excit. pulse
* this is achieved by an inverse gradient right after the excitation pulse
freq_1_2_1=-frs_1_1*128*pulse_1_1_1/2

select_[5 7]=[-1 1]

* set the durations of all crusher gradient pulses to zero,
* essentially removing them from the pulse sequence
* this line and the line befor should be commented out if the last three lines are uncommented
pulse_1_[4 8 10 12]_1=0

* use phase averaging insted of explicit coherence selection
*ave_par1d phi1/0:90:359/
*ave_par2d phi2/0:90:359/
*freq_1_[4 8 10 12]_1=(phi[1 1 2 2]/360)/0.001

******* Options ************************************************
rho0               F1z
observables        F1p
EulerAngles        *
n_gamma            *
line_broaden(Hz)   0 2.5
zerofill           *
FFT_dimensions     1
*************************
-- one can set the frequency of the selective 90 from the command line (or from a script) by using the -var option. For example,
spinev press-mi -varfrs_1_1=0.5
sets the frequency offset for this pulse to 0.5 kHz
-- ppm_ref_offs_1 is the offset, kHz, of the ppm-reference compound with respect to the Reference Frequency. (The frequency offsets of all pulses are also given with respect to this Reference Frequency).
The assignment
ppm_ref_offs_1=0.16822*3.5
sets the ppm-reference scale such that the Reference Frequency is at the 3.5 ppm on this scale

A jump-start description of this simulation for a novice SpinEvolution user

  • the experiment is described in the file named press-mi; the molecule (chemical shifts and j-couplings) – in two additional files; selective pulses are specified by the files e.pwr (excitation pulse shape), a.pwr (refocusing pulse shape), and t128.tm and t200.tm (durations of each pulse in the shape).
  • the pulse sequence of the experiment is represented as a sequence consisting of 14 “elementary” pulse sequences, numbered 1 to 14. They are separated from each other by parentheses on the timing(usec) line. Sequences 1 to 13 belong to dimension zero, meaning that each of them is repeated exactly the same number of times (in this experiment – once) for each observed data point. The sequence 14 (a 500 usec delay) is incremented in dimension 1, from 0 to 8191 times, for each observed data point. Thus, we a have here a 1D experiment consisting of some preparation period followed by a FID detection.
  • all sequences, except for 1, 6, and 11 (i.e. the selective pulses), consist of just one pulse; the excitation shape consists of 128 pulses, and the refocusing shapes consist of 200 pulses
  • most of the things in the “Pulse Sequence” section of the input file are self-explanatory
  • all pulse durations, powers, phases, and frequencies set in this section can be overwritten in the Variables section that follows. Sometimes, it is convenient to put zeros for some values in the Pulse Sequence section, and then specify the actual values in the Variables section
  • all lines starting with an asterisk within this section are treated as comments
  • pulse_1_[1 6 11]=[20 25 25] is a macro that is expanded into three different lines: pulse_1_1=20pulse_1_6=25 pulse_1_11=25 pulse_n_s is a vector of pulse lengths for sequence s on channel n (there is just one channel in this experiment). Thus, each step in the excitation pulse (sequence 1) is set to 20 usec, and in the refocusing pulses (sequences 6 and 11) – to 25 usec
  • psf_n_s is the “power scaling factor” for sequence s on channel n; the default value for these factors (i.e. if it is not specified is 1); here, it is used to convert the pulse shape amplitudes, given in mT in the *.pwr files, to kHz
  • the line ppm_ref_offs_1=0.16822*3.5 sets the ppm scale (used in the myo-inositol.cs file) with respect to the spectrometer frequency offsets scale; 0.16822 factor converts ppm to kHz
  • frs_n_s is the frequency shift for sequence s on channel n; all frequency offsets specified at the freq_offs(kHz) line (or the via the freq_n_s_p variable) are shifted by these values. Thus, the line (actually, a macro for three different lines) frs_1_[1 6 11]=[0.5 0 0.5] sets the frequency offsets of the pulses during the pulse shapes to 0.5 kHz for the excitation and the second refocusing pulse, and to 0 kHz – for the fist refocusing pulse; in the experiment, these offsets are dependent on the spatial location of the point and are controlled by the gradients
  • Using scan_par frs_1_6/-1:0.1:1/ frs_1_[1 11]=[0.5 0.5] instead of frs_1_[1 6 11]=[0.5 0 0.5]) would lead to scanning frs_1_6 from -1 to 1 kHz, in steps of 0.1 kHz (which is equivalent to scanning the localization point along the direction of the gradient during the 1st refocusing pulse).
  • The line freq_1_2_1=-frs_1_1*128*pulse_1_1_1/2 sets the frequency of the 1-usec pulse during sequence 2 to such a value that it would refocus the position-dependent phase created during the excitation pulse; it is equivalent to the inverse gradient pulse given in the actual experiment (pulse_n_s_p here is the duration of pulse p of the sequence s on channel n; so, 128*pulse_1_1_1 is the duration of the whole pulse shape, which consists of 128 pulses)
  • The coherence pathway for PRESS is:0 ->(excitation)-> -1 -> (refocus1) -> +1 -> (refocus2) -> -1 -> observationthe lineselect_[5 7]=[-1 1]selects coherences of order -1 during sequence 5, and of order +1 during sequence 7; (and kills all other coherences during these sequences); this is equivalent to independent crusher gradient pairs, each consisting of equal strength and duration gradients before and after the refocusing pulses
  • alternatively, the effects of the crusher gradients can be modeled more explicitly:the following lines could be used to loop the variables phi1 and phi2 (independently) through values (0,90,180, 270) and set the frequencies during the crusher gradients (sequences 4, 8, 10, and 12) to the values leading to the appropriate averaging ave_par1d phi1/0:90:359/ ave_par2d phi2/0:90:359/ freq_1_[4 8 10 12]_1=(phi[1 1 2 2]/360)/0.001 The linepulse_1_[4 8 10 12]_1=0 must be commented out in this case
  • The Options section:
  • the lines rho0 F1z observables F1p are self-explanatory
  • the line line_broaden(Hz) 0 2.5 tells to apodize FID with 0 Hz lorentzian line broadening and 2.5 Hz gaussian
  • FFT_dimensions 1 specifies to Fourier-transform FID along dimension 1
  • The simulation is run from the command line asspinev press-miThe output (i.e. the spectrum in this case) is saved as press-mi_re.dat and press-mi_im.dat files
  • Files:
mio-inositol.cs
3.5217
4.0538
3.5217
3.6144
3.2690
3.6144
0.1
mio-inositol.j
1 2 2.889
1 6 9.998
2 3 3.006 
3 4 9.997
4 5 9.485
5 6 9.482
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