This section contains a brief alphabetic list of the pre-coded pulse sequences supplied with Spinach. If your particular sequence is not listed below, or if you have invented something that is worthy of broad public adoption, drop us a note – we are always interested in expanding Spinach capabilities. With the exceptions noted below, the sequences must be invoked via liquid, crystal, powder and roadmap wrapper functions (see the example set).
acquire.m – simple forward time evolution with signal acquisition.
traject.m - simple forward time evolution, trajectory is returned.
slowpass.m – slow passage detection - calculates spectrum values at the user specified frequency positions using the Fourier transform of the Liouville - von Neumann equation. The biggest advantage over the fid + fft style detection is easy parallelization and the possibility of getting spectrum values at specific frequencies without recalculating the entire free induction decay.
hp_acquire.m – standard hard pulse acquire sequence. The user must supply the pulse operator, the pulse duration and the initial condition.
sp_acquire.m - a pulse-acquire sequence with a soft pulse.
holeburn.m - hole burning experiment.
levelpop.m - energy levels and their populations.
clip_hsqc.m – CLIP-HSQC pulse sequence.
cosy.m – phase-sensitive COSY pulse sequence.
crosspol.m – cross-polarization experiment.
dqf_cosy.m – phase-sensitive double-quantum filtered COSY pulse sequence
hetcor.m – magnitude mode HETCOR pulse sequence.
hmqc.m – magnitude mode HMQC pulse sequence.
hnco.m – Phase-sensitive HNCO pulse sequence from the paper by Lewis Kay and co-authors, using the bidirectional propagation method (paper in press). The sequence is hard-wired to work on 1H, 13C, 15N labelled proteins.
hncoca.m – Phase-sensitive HNCO pulse sequence from the paper by Bax and Ikura, using the bidirectional propagation method (paper in press). The sequence is hard-wired to work on 1H, 13C, 15N labelled proteins.
hsqc.m – phase-sensitive HSQC pulse sequence.
lcosy.m – localized COSY pulse sequence.
cn2d.m – CN2D experiment under MAS. See the function header for further information.
noesy.m – phase-sensitive homonuclear NOESY pulse sequence.
roesy.m - phase-sensitive homonuclear ROESY pulse sequence.
noesyhsqc.m – phase-sensitive NOESY-HSQC pulse sequence from the paper by Marion and co-authors. The sequence is hard-wired to 1H, 15N, 1H.
Spatially encoded NMR
1. Ultra-fast NMR:
spencosy.m - ultrafast COSY experiment.
spendosy.m - ultrafast DOSY experiment.
spendosycosy.m - ultrafast 3D DOSY-COSY experiment.
2. Phase sensitive NMR:
diag_psyche_zfilters.m - Phase-sensitive homonuclear DIAG pulse sequence.
3. Pure-shift NMR:
psyche_1d.m - PSYCHE 1D pulse sequence.
4. Diffusion weighting NMR:
dosy_oneshot.m - One-shot DOSY pulse sequence.
pfg_spin_echo.m - Pulsed field gradient spin echo sequence.
pfg_stim_echo.m - Pulsed field gradient stimulated spin echo sequence.
bpp_stim_echo.m - Bipolar pulse pair stimulated spin echo sequence.
Overtone NMR experiments
overtone_a.m - overtone signal acquisition.
overtone_cp.m - overtone cross-polarisation.
overtone_pa.m - overtone pulse-acquire.
overtone_dante.m - overtone DANTE.
endor_cw.m – continuous-wave ENDOR pulse sequence.
endor_mims.m – Mims ENDOR pulse sequence.
endor_davies.m - Davies ENDOR pulse sequence.
eseem.m – ESEEM pulse sequence.
hyscore.m – HYSCORE experiment.
oopeseem.m - out-of-phase ESEEM expariment.
rapidscan.m - ESR rapid field scan experiment.
deer_3p_hard_echo.m - echo diagnostocs for ideal three-pulse DEER.
deer_3p_hard_deer.m - ideal three-pulse DEER.
deer_3p_soft_deer.m - three-pulse DEER with realistic pulses and orientation selection.
deer_3p_soft_hole.m - pulse hole diagnostics for three-pulse DEER with realistic pulses and orientation selection.
deer_3p_soft_diag.m - full diagnostics suite for three-pulse DEER with realistic pulses and orientation selection.
deer_4p_soft_deer.m - four-pulse DEER with realistic pulses and orientation selection.
deer_4p_soft_hole.m - pulse hole diagnostics for four-pulse DEER with realistic pulses and orientation selection.
deer_4p_soft_diag.m - full diagnostics suite for four-pulse DEER with realistic pulses and orientation selection.
dnp_field_scan.m – field scan steady-state DNP experiment.
dnp_freq_scan.m – frequency scan steady-state DNP experiment.
solid_effect.m – large-scale simulation of solid effect DNP.
masdnp.m - magic angle spinning DNP.
ipcs.m – spin density recovery from pseudocontact shifts. See function header for further information.
ippcs.m – point electron model fitting to PCS data. See the function header for further information.
kpcs.m – PCS calculation using Kuprov equation. See the function header for further information.
hfc2pcs.m - computes pseudocontact shifts from hyperfine couplings and susceptibility tensors.
hfc2pms.m - computes paramagnetic shifts (contact + pseudocontact) from hyperfine couplings and susceptibility data.
pms2chi.m - extracts magnetic susceptibility tensors from paramagnetic shift data.
pcs2chi.m - extracts rank 2 components of the magnetic susceptibility tensors from pseudocontact shift data.
ppcs.m - Computes pseudocontact shift from a point electron centre at the nuclear coordinates supplied.
rydmr.m – singlet-singlet RYDMR experiment with exponential recombination function, as described in the paper by Timmel and co-authors.
zerofield.m - gamma-weighted pulse-acquire sequence in zero field.
crazed.m – CRAZED sequence, implemented as described in Warren Warren's paper.