Difference between revisions of "Built-in experiments"

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[[acquire.m]] – simple forward time evolution with signal acquisition.
 
[[acquire.m]] – simple forward time evolution with signal acquisition.
 +
 +
[[cpmg.m]] - CPMG echo train with detection.
  
 
[[holeburn.m]] - hole burning experiment.
 
[[holeburn.m]] - hole burning experiment.
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[[impound.m]] - captures what it receives from the context function and returns it to the user.
 
[[impound.m]] - captures what it receives from the context function and returns it to the user.
  
−
[[levelpop.m]] - energy levels and their populations.
+
[[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.
 
[[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.
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[[traject.m]] - simple forward time evolution, trajectory is returned as a stack of density matrices.
 
[[traject.m]] - simple forward time evolution, trajectory is returned as a stack of density matrices.
  
−
==NMR experiments==
+
==Liquid state NMR experiments==
 +
 
 +
===General pulse sequences===
  
 
[[clip_hsqc.m]] – CLIP-HSQC pulse sequence.  
 
[[clip_hsqc.m]] – CLIP-HSQC pulse sequence.  
  
−
[[cn2d_sq.m]] – CN2D experiment under MAS, single-quantum.
+
[[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.
  
−
[[cn2d_dq.m]] – CN2D experiment under MAS, double-quantum.
+
[[deptq.m]] - DEPTQ pulse sequence.
  
−
[[cosy.m]] – phase-sensitive COSY pulse sequence.  
+
[[dqf_cosy.m]] – phase-sensitive double-quantum filtered COSY pulse sequence.
  
−
[[crosspol.m]] – cross-polarization experiment.  
+
[[ecosy.m]] - Phase-sensitive E.COSY pulse sequence.
  
−
[[dqf_cosy.m]] – phase-sensitive double-quantum filtered COSY pulse sequence
+
[[hetcor.m]] – magnitude mode HETCOR pulse sequence.
  
−
[[hetcor.m]] – magnitude mode HETCOR pulse sequence.  
+
[[hmbc.m]] - HMBC pulse sequence.
  
 
[[hmqc.m]] – magnitude mode HMQC pulse sequence.  
 
[[hmqc.m]] – magnitude mode HMQC pulse sequence.  
  
−
[[hnco.m]] – Phase-sensitive HNCO pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.  
+
[[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.
  
−
[[hncoca.m]] – Phase-sensitive HNCO pulse sequence. Hard-wired to work on 1H, 13C, 15N labelled proteins.  
+
[[inept.m]] - INEPT pulse sequence.
  
−
[[hsqc.m]] – phase-sensitive HSQC pulse sequence.
+
[[inv_rec.m]] - inversion-recovery sequence.
 +
 
 +
[[mqs.m]] - 2D multiple-quantum NMR pulse sequence.
  
−
[[lcosy.m]] – localized  COSY pulse sequence.  
+
[[mqs_refocus.m]] - 2D multiple-quantum NMR pulse sequence.
  
 
[[noesy.m]] – phase-sensitive homonuclear NOESY pulse sequence.
 
[[noesy.m]] – phase-sensitive homonuclear NOESY pulse sequence.
  
−
[[noesyhsqc.m]] – phase-sensitive NOESY-HSQC pulse sequence. Hard-wired to 1H, 15N, 1H.
+
[[pansy_cosy.m]] - PANSY-COSY pulse sequence.
 +
 
 +
[[pansy_triple.m]] - Triple-channel PANSY pulse sequence.
  
 
[[roesy.m]] - phase-sensitive homonuclear ROESY pulse sequence.
 
[[roesy.m]] - phase-sensitive homonuclear ROESY pulse sequence.
 +
 +
[[sat_rec.m]] - saturation-recovery sequence.
  
 
[[tocsy.m]] - amplitude-mode homonuclear TOCSY.
 
[[tocsy.m]] - amplitude-mode homonuclear TOCSY.
  
−
==Spatially encoded NMR==
+
===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.
 +
 
 +
[[cp_acquire_soft.m]] - Cross-polarisation NMR experiment.
 +
 
 +
[[cp_contact_soft.m]] - Cross-polarisation NMR experiment with a soft pulse.
 +
 
 +
[[cp_contact_hard.m]] - Cross-polarisation NMR experiment in the rotating frame.
  
−
===Ultrafast and pure-shift NMR===
+
[[dante.m]] - DANTE pulse sequence.
  
−
[[spencosy.m]] - ultrafast COSY experiment.
+
[[fslghetcor.m]] - Heteronuclear correlation MAS NMR experiment with frequency-switched Lee-Goldburg homonuclear decoupling.
  
−
[[spendosy.m]] - ultrafast DOSY experiment.
+
[[mqmas.m]] - 2D multiple-quantum MAS pulse sequence for quadrupolar nuclei.
  
−
[[dosy_oneshot.m]] - one-shot DOSY pulse sequence.
+
[[nqr_pa.m]] - nuclear quadrupole resonance soft pulse-acquire experiment.
  
−
[[spendosycosy.m]] - ultrafast 3D DOSY-COSY experiment.
+
[[pdsd.m]] - 2D proton-driven spin diffusion experiment.
  
−
[[spendosy_keeler_fit.m]] - original Keeler model data processing for SPEN DOSY.
+
[[respiration.m]] - RESPIRATION CP pulse sequence.
  
−
[[spendosy_keeler_fit_corr.m]] - corrected Keeler model data processing for SPEN DOSY.
+
[[wise.m]] - WISE (wideline separation) pulse sequence.
  
−
[[spendosy_frydman_fit.m]] - original Frydman model data processing for SPEN DOSY.
+
==Spatially encoded NMR==
  
−
[[spendosy_keeler_fit_corr.m]] - corrected Frydman model data processing for SPEN DOSY.
+
===Ultrafast, pure-shift, and diffusion NMR===
  
−
[[spendosy_processing1s.m]] - SPEN DOSY processing, one signal.
+
[[spencosy.m]] - ultrafast COSY experiment.
  
−
[[spendosy_processing2s.m]] - SPEN DOSY processing, two signals.
+
[[spendosy.m]] - ultrafast DOSY experiment.
  
−
[[stejskal_tanner_analysis.m]] - Stejskal-Tanner analysis of diffusion data.
+
[[spendosycosy.m]] - ultrafast 3D DOSY-COSY experiment.
  
−
[[psyche_1d.m]] - PSYCHE 1D pulse sequence.
+
[[psyche.m]] - PSYCHE 1D pulse sequence.
  
−
[[diag_psyche_zfilters.m]] - Phase-sensitive homonuclear DIAG pulse sequence.
+
[[psycosy.m]] - spatially encoded pure shift COSY.
  
−
===Diffusion NMR===
+
[[ufmq.m]] - ultrafast multiple-quantum NMR pulse sequence.
  
−
[[pfg_spin_echo.m]] - Pulsed field gradient spin echo sequence.
+
[[st_ideal.m]] - ideal Stejskal-Tanner pulse sequence.
  
−
[[pfg_stim_echo.m]] - Pulsed field gradient stimulated spin echo sequence.
+
[[dosy_oneshot.m]] - Oneshot DOSY pulse sequence.
  
−
[[bpp_stim_echo.m]] - Bipolar pulse pair stimulated spin echo sequence.
+
[[idosyzs.m]] - Zangger-Sterk pure shift iDOSY pulse sequence.
  
 
===Gradient signal suppression===
 
===Gradient signal suppression===
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[[dpfgse_suppress.m]] - DPFGSE signal suppression
 
[[dpfgse_suppress.m]] - DPFGSE signal suppression
 +
 +
===Microfluidics===
 +
 +
[[simple_flow.m]] - time evolution trajectory in a microfluidics context
  
 
==Magnetic resonance imaging==
 
==Magnetic resonance imaging==
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==ESR experiments==
 
==ESR experiments==
 +
 +
[[deer_3p_hard_echo.m]] - echo diagnostics 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.
  
 
[[endor_cw.m]] – continuous-wave ENDOR pulse sequence.  
 
[[endor_cw.m]] – continuous-wave ENDOR pulse sequence.  
  
−
[[endor_mims.m]] – Mims ENDOR pulse sequence.  
+
[[endor_davies.m]] - Davies ENDOR pulse sequence.
 +
 
 +
[[endor_mims.m]] – Mims ENDOR pulse sequence.
 +
 
 +
[[endor_mims_echo.m]] - Stimulated echo diagnostics for the Mims ENDOR sequence.
  
−
[[endor_davies.m]] - Davies ENDOR pulse sequence.
+
[[endor_mims_ideal.m]] - Mims ENDOR sequence with ideal electron pulses.
  
 
[[eseem.m]] – ESEEM pulse sequence.
 
[[eseem.m]] – ESEEM pulse sequence.
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[[rapidscan.m]] - ESR rapid field scan experiment.
 
[[rapidscan.m]] - ESR rapid field scan experiment.
  
−
==DEER/PELDOR experiments==
+
[[ridme.m]] - RIDME pulse sequence.
  
−
[[deer_3p_hard_echo.m]] - echo diagnostocs for ideal three-pulse DEER.
+
[[sifter.m]] - SIFTER experiment
  
−
[[deer_3p_hard_deer.m]] - ideal three-pulse DEER.
+
[[deer_analyt.m]] - Analytical expression for a DEER trace for two spins in the presence of dipolar and exchange (EPR) or J (NMR) coupling.
  
−
[[deer_3p_soft_deer.m]] - three-pulse DEER with realistic pulses and orientation selection.
+
[[rydmr_exp.m]] - Singlet-singlet RYDMR experiment with exponential recombination function.
  
−
[[deer_3p_soft_hole.m]] - pulse hole diagnostics for three-pulse DEER with realistic pulses and orientation selection.
+
==DNP experiments==
  
−
[[deer_3p_soft_diag.m]] - full diagnostics suite for three-pulse DEER with realistic pulses and orientation selection.
+
[[beamdnp.m]] - Beam DNP experiment.
  
−
[[deer_4p_soft_deer.m]] - four-pulse DEER with realistic pulses and orientation selection.
+
[[dnp_field_scan.m]] – magnetic field scan steady-state DNP experiment.
  
−
[[deer_4p_soft_hole.m]] - pulse hole diagnostics for four-pulse DEER with realistic pulses and orientation selection.
+
[[dnp_freq_scan.m]] – microwave frequency scan steady-state DNP experiment.
  
−
[[deer_4p_soft_diag.m]] - full diagnostics suite for four-pulse DEER with realistic pulses and orientation selection.
+
[[dnp_time_dep.m]] - time-domain spin dynamics under microwave irradiation.
  
−
==DNP experiments==
+
[[masdnp.m]] - magic angle spinning DNP.
  
−
[[dnp_field_scan.m]] – field scan steady-state DNP experiment.
+
[[noveldnp.m]] - NOVEL DNP and pulsed solid effect DNP.
  
−
[[dnp_freq_scan.m]] – frequency scan steady-state DNP experiment.
+
[[noveldnp_steady.m]] - steady-state NOVEL DNP and pulsed solid effect DNP.
  
 
[[solid_effect.m]] – large-scale simulation of solid effect DNP.
 
[[solid_effect.m]] – large-scale simulation of solid effect DNP.
  
−
[[masdnp.m]] - magic angle spinning DNP.
+
[[topdnp.m]] - time-optimised DNP pulse sequence.
 +
 
 +
[[xixdnp.m]] - TPPM DNP and its special case X-inverse-X (XiX) DNP experiment.
 +
 
 +
[[xixdnp_steady.m]] - TPPM DNP and its special case X-inverse-X (XiX) DNP experiment, steady-state version.
  
 
==Paramagnetic NMR spectroscopy==
 
==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.  
 
[[eqmag.m]] - molar magnetization vector at the thermal equilibrium.  
Line 171: Line 269:
 
[[hfc2pms.m]] - computes paramagnetic shifts (contact + pseudocontact) from hyperfine couplings and susceptibility data.
 
[[hfc2pms.m]] - computes paramagnetic shifts (contact + pseudocontact) from hyperfine couplings and susceptibility data.
  
−
[[ipcs.m]] – spin density recovery from pseudocontact shifts. See function header for further information.
+
[[ipcs.m]] – tag probability density recovery from pseudocontact shifts..
  
−
[[ippcs.m]] – point electron model fitting to PCS data. See the function header for further information.
+
[[ippcs.m]] – point electron model fitting to PCS data.
  
−
[[kpcs.m]] – PCS calculation using Kuprov equation. See the function header for further information.
+
[[kpcs.m]] – PCS calculation using Kuprov equation.  
  
 
[[pms2chi.m]] - extracts magnetic susceptibility tensors from paramagnetic shift data.
 
[[pms2chi.m]] - extracts magnetic susceptibility tensors from paramagnetic shift data.
Line 184: Line 282:
  
 
[[ppcs.m]] - Computes pseudocontact shift from a point electron centre at the nuclear coordinates supplied.
 
[[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.
  
 
==Exotica==
 
==Exotica==
−
[[crazed.m]] – CRAZED sequence, implemented as described in Warren Warren's paper.
+
[[rydmr.m]] – singlet-singlet RYDMR experiment with exponential recombination function.
−
 
 
−
[[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.
 
[[zerofield.m]] - gamma-weighted pulse-acquire sequence in zero field.
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[[zulf_abrupt.m]] - zero-field NMR with an abrupt field drop.
 
[[zulf_abrupt.m]] - zero-field NMR with an abrupt field drop.
  
 +
==Hyperpolarisation and DNP experiments==
 +
 +
[[topdnp_steady.m]] - Time-optimised pulsed DNP experiment from: https://doi.org/10.1126/sciadv.aav6909 (a steady state version).
  
−
''Version 2.1, authors: [[Ilya Kuprov]]''
+
''Version 2.5, authors: [[Ilya Kuprov]]''

Latest revision as of 19:34, 6 June 2026

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.

ecosy.m - Phase-sensitive E.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.

cp_acquire_soft.m - Cross-polarisation NMR experiment.

cp_contact_soft.m - Cross-polarisation NMR experiment with a soft pulse.

cp_contact_hard.m - Cross-polarisation NMR experiment in the rotating frame.

dante.m - DANTE pulse sequence.

fslghetcor.m - Heteronuclear correlation MAS NMR experiment with frequency-switched Lee-Goldburg homonuclear decoupling.

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

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

pdsd.m - 2D proton-driven spin diffusion experiment.

respiration.m - RESPIRATION CP pulse sequence.

wise.m - WISE (wideline separation) 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

Microfluidics

simple_flow.m - time evolution trajectory in a microfluidics context

Magnetic resonance imaging

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

cpmg_dec.m - CPMG echo train epi_2d.m - 2D (spatial) echo planar imaging sequence

epi_3d.m - Diffusion weighted 3D echo planar imaging pulse sequence.

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

grad_echo.m - simple gradient echo pulse sequence

phase_enc_2d.m - 2D (spatial) phase encoded imaging.

phase_enc_3d.m - 3D (spatial) imaging with slice selection followed by phase-encoded acquisition

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_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

deer_3p_hard_echo.m - echo diagnostics 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.

endor_cw.m – continuous-wave ENDOR pulse sequence.

endor_davies.m - Davies ENDOR pulse sequence.

endor_mims.m – Mims ENDOR pulse sequence.

endor_mims_echo.m - Stimulated echo diagnostics for the Mims ENDOR sequence.

endor_mims_ideal.m - Mims ENDOR sequence with ideal electron pulses.

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_analyt.m - Analytical expression for a DEER trace for two spins in the presence of dipolar and exchange (EPR) or J (NMR) coupling.

rydmr_exp.m - Singlet-singlet RYDMR experiment with exponential recombination function.

DNP experiments

beamdnp.m - Beam DNP experiment.

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.

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

noveldnp_steady.m - steady-state 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 - TPPM DNP and its special case X-inverse-X (XiX) DNP experiment.

xixdnp_steady.m - TPPM DNP and its special case X-inverse-X (XiX) DNP experiment, steady-state version.

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.

Exotica

rydmr.m – singlet-singlet RYDMR experiment with exponential recombination function.

zerofield.m - gamma-weighted pulse-acquire sequence in zero field.

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

Hyperpolarisation and DNP experiments

topdnp_steady.m - Time-optimised pulsed DNP experiment from: https://doi.org/10.1126/sciadv.aav6909 (a steady state version).

Version 2.5, authors: Ilya Kuprov

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