Built-in experiments

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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).

General experiments

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.

NMR experiments

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.

ESR experiments

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/PELDOR experiments

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 experiments

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.

Paramagnetic shift

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.

Exotica

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.