Difference between revisions of "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).
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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.  
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Unless stated otherwise in the experiment description, all of the functions listed below below should be invoked via a wrapper function that sets the appropriate (solid, liquid, ''etc.'') simulation [[kernel contexts|context]].
  
 
==General experiments==
 
==General experiments==

Revision as of 18:58, 29 December 2017

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.

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

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.

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

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

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. Hard-wired to work on 1H, 13C, 15N labelled proteins.

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

hsqc.m – phase-sensitive HSQC pulse sequence.

lcosy.m – localized COSY pulse sequence.

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

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

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

tocsy.m - amplitude-mode homonuclear TOCSY.

Spatially encoded NMR

Ultrafast and pure-shift NMR

spencosy.m - ultrafast COSY experiment.

spendosy.m - ultrafast DOSY experiment.

dosy_oneshot.m - one-shot DOSY pulse sequence.

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

spendosy_keeler_fit.m - original Keeler model data processing for SPEN DOSY.

spendosy_keeler_fit_corr.m - corrected Keeler model data processing for SPEN DOSY.

spendosy_frydman_fit.m - original Frydman model data processing for SPEN DOSY.

spendosy_keeler_fit_corr.m - corrected Frydman model data processing for SPEN DOSY.

spendosy_processing1s.m - SPEN DOSY processing, one signal.

spendosy_processing2s.m - SPEN DOSY processing, two signals.

stejskal_tanner_analysis.m - Stejskal-Tanner analysis of diffusion data.

psyche_1d.m - PSYCHE 1D pulse sequence.

diag_psyche_zfilters.m - Phase-sensitive homonuclear DIAG pulse sequence.

Diffusion NMR

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.

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.

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 spectroscopy

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 – 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.

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.