Built-in experiments

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This section contains a list of the pre-programmed pulse sequences supplied with Spinach. Everything is open-source, so feel free to hack and modify as appropriate. If your particular sequence is not listed below, or if you have written something that is worthy of broad public adoption, drop us a note – we are always interested in expanding Spinach capabilities.

Unless stated otherwise in the experiment description, all of the functions listed below below should be invoked via a kernel context function that sets the appropriate (solid, liquid, etc.) simulation infrastructure.

General experiments

acquire.m – simple forward time evolution with signal acquisition.

cpmg.m - CPMG echo train with detection.

holeburn.m - hole burning experiment.

hp_acquire.m – standard hard pulse acquire sequence. The user must supply the pulse operator, the pulse duration and the initial condition.

impound.m - captures what it receives from the context function and returns it to the user.

relaxan.m - automated relaxation theory analysis.

slowpass.m – 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.

sp_acquire.m - a pulse-acquire sequence with a soft pulse.

traject.m - simple forward time evolution, trajectory is returned as a stack of density matrices.

Liquid state NMR experiments

General pulse sequences

clip_hsqc.m – CLIP-HSQC pulse sequence.

coloc.m - COLOC pulse sequence.

cosy.m – phase-sensitive COSY pulse sequence.

crazed.m - CRAZED sequence for distant dipolar effects

ct_cosy.m - constant-time COSY pulse sequence.

ct_hsqc.m - Constant-time phase-sensitive HSQC pulse sequence.

dept.m - DEPT pulse sequence.

deptq.m - DEPTQ pulse sequence.

dqf_cosy.m – phase-sensitive double-quantum filtered COSY pulse sequence

hetcor.m – magnitude mode HETCOR pulse sequence.

hmbc.m - HMBC pulse sequence.

hmqc.m – magnitude mode HMQC pulse sequence.

hoesy.m - phase-sensitive heteronuclear NOESY sequence.

hsqc.m – phase-sensitive HSQC pulse sequence.

inadequate.m - 1D INADEQUATE pulse sequence.

inadequate_2d.m - 2D INADEQUATE pulse sequence.

inept.m - INEPT pulse sequence.

inv_rec.m - inversion-recovery sequence.

mqs.m - 2D multiple-quantum NMR pulse sequence.

mqs_refocus.m - 2D multiple-quantum NMR pulse sequence.

noesy.m – phase-sensitive homonuclear NOESY pulse sequence.

pansy_cosy.m - PANSY-COSY pulse sequence.

pansy_triple.m - Triple-channel PANSY pulse sequence.

roesy.m - phase-sensitive homonuclear ROESY pulse sequence.

sat_rec.m - saturation-recovery sequence.

tocsy.m - amplitude-mode homonuclear TOCSY.

Protein pulse sequences

hcanh.m - H(CA)NH pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.

hcch_tocsy.m - HCCH TOCSY pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.

hcch_cosy.m - HCCH-COSY pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.

hnco.m – HNCO pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.

hnca.m - HNCA pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.

hncaco.m - HN(CA)CO pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.

hncoca.m – HNCOCA pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.

noesyhsqc.m – phase-sensitive NOESY-HSQC pulse sequence. Hard-wired to work on 1H, 15N labelled proteins.

Singlet states

m2s.m - magnetisation to singlet state.

s2m.m - singlet state to magnetisation.

Residual dipolar couplings

rdc_fit.m - fitting residual dipolar coupling

xyz2rdc.m - Cartesian coordinates and order matrix into residual dipolar coupling

Solid state NMR experiments

cn2d_sq.m – CN2D experiment under MAS, single-quantum.

cn2d_dq.m – CN2D experiment under MAS, double-quantum.

crosspol.m – cross-polarization experiment.

dante.m - DANTE pulse sequence.

mqmas.m - 2D multiple-quantum MAS pulse sequence for quadrupolar nuclei.

nqr_pa.m - nuclear quadrupole resonance soft pulse-acquire experiment.

respiration.m - RESPIRATION CP pulse sequence.

Spatially encoded NMR

Ultrafast, pure-shift, and diffusion NMR

spencosy.m - ultrafast COSY experiment.

spendosy.m - ultrafast DOSY experiment.

spendosycosy.m - ultrafast 3D DOSY-COSY experiment.

psyche.m - PSYCHE 1D pulse sequence.

psycosy.m - spatially encoded pure shift COSY.

ufmq.m - ultrafast multiple-quantum NMR pulse sequence.

st_ideal.m - ideal Stejskal-Tanner pulse sequence.

dosy_oneshot.m - Oneshot DOSY pulse sequence.

idosyzs.m - Zangger-Sterk pure shift iDOSY pulse sequence.

Gradient signal suppression

dpfgse_select.m - DPFGSE signal selection

dpfgse_suppress.m - DPFGSE signal suppression

Magnetic resonance imaging

basic_1d_hard.m - basic 1D imaging with a hard pulse and a gradient

cpmg_dec.m - CPMG echo train

dwi.m - 2D (spatial) diffusion weighted imaging sequence

epi.m - 2D (spatial) echo planar imaging sequence

fse.m - 2D (spatial) fast spin echo sequence

grad_echo.m - simple gradient echo pulse sequence

phase_enc.m - 2D (spatial) phase encoded imaging.

press_1d.m - 1D (spatial) PRESS sequence

press_2d.m - 2D (spatial) PRESS sequence

press_voxel_1d.m - voxel selection diagnostics for 1D (spatial) PRESS pulse sequence

press_voxel_2d.m - voxel selection diagnostics for 2D (spatial) PRESS pulse sequence

press_voxel_3d.m - voxel selection diagnostics for 2D (spatial) PRESS pulse sequence

slice_phase_enc.m - 3D (spatial) imaging with slice selection followed by phase-encoded acquisition

slice_select_1d.m - slice selection diagnostics

spin_echo.m - simple spin echo pulse sequence

spiral.m - 2D (spatial) imaging with spiral readout

udd_dec.m - Uhrig Dynamic Decoupling (UDD) echo train

uhrig_times.m - timing sequence for UDD echo train

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.

fieldsweep.m - field sweep ESR experiment using steady state formalism.

hyscore.m – HYSCORE experiment.

oopeseem.m - out-of-phase ESEEM experiment.

rapidscan.m - ESR rapid field scan experiment.

ridme.m - RIDME pulse sequence.

sifter.m - SIFTER 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 – magnetic field scan steady-state DNP experiment.

dnp_freq_scan.m – microwave frequency scan steady-state DNP experiment.

dnp_time_dep.m - time-domain spin dynamics under microwave irradiation.

masdnp.m - magic angle spinning DNP.

novel_se.m - NOVEL DNP and pulsed solid effect DNP.

solid_effect.m – large-scale simulation of solid effect DNP.

topdnp.m - time-optimised DNP pulse sequence.

xixdnp.m - X-inverse-X (XiX) DNP experiment.

Paramagnetic NMR spectroscopy

centroid.m - centre of mass point of a 3D probability density in a cube.

csa2racs.m - residual anisotropic chemical shift.

eqmag.m - molar magnetization vector at the thermal equilibrium.

fieldscan_enlev.m - energy levels as a function of the magnetic field.

fieldscan_magn.m - Z magnetisation in a finite-speed field sweep.

geffect.m - Effective g-tensor for a user-specified Kramers doublet.

hfc2pcs.m - computes pseudocontact shifts from hyperfine couplings and susceptibility tensors.

hfc2pms.m - computes paramagnetic shifts (contact + pseudocontact) from hyperfine couplings and susceptibility data.

ipcs.m – tag probability density recovery from pseudocontact shifts..

ippcs.m – point electron model fitting to PCS data.

kpcs.m – PCS calculation using Kuprov equation.

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.

pcs_combi_fit.m - PCS data fitting with ambiguous assignments.

ppcs.m - Computes pseudocontact shift from a point electron centre at the nuclear coordinates supplied.

probmax.m - maximum point of a 3D probability density in a cube.


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.

zulf_abrupt.m - zero-field NMR with an abrupt field drop.

Version 2.5, authors: Ilya Kuprov