This page is a mirror of Varian's page describing pulse sequences distributed in BioPack, as updated in June 2008.  The author of this page is Rolf Kyburz at Varian (rolf.kyburz@varianinc.com).

BioPack Pulse Sequences for Proteins:

Common Name Sequence Name(s)
PRESAT - includes PRESAT, WET, shaped-pulse PRESAT, jump-return, watergate (soft, 3919, W5) water  
C13 spin echo C13spinecho  
C13 observe C13observe  
C13 gradient COSY C13gcosy  
C13 DQF COSY C13dqcosy  
Saturation Transfer Difference 1D satxfer1D  
watergate COSY wgcosy  
watergate DQFCOSY wgdqfcosy  
watergate NOESY wgnoesy  
watergate ROESY wgroesy  
watergate TOCSY wgtocsy  
wet NOESY wnoesy  
wet ROESY wroesy  
"quiet" NOESY qwnoesy, qwnoesyA  
CPMG-NOESY CPMGnoesy  
SS-NOESY SSnoesy  
NOESY-C_chirp_purge_lek_v3a noesyCA  
C and/or N filtered NOESY CNfilnoesy  
magic-angle DQFCOSY gmacosy  
z-filtered DIPSI-TOCSY zdipsitocsy  
CLEANEX N15-HSQC gCLNfhsqc, gCLNfhsqcA  
Fast N15-HSQC gNfhsqc, gNfhsqcA  
Fast N15-HSQC with Homodecoupling gNfhsqcHD, gNfhsqcHDA  
Fast N15-IPAP-HSQC with Homodec. gNfhsqc_IPAPHD, gNfhsqc_IPAPHDA  
Fast Fast HNCO for C=O labeled proteins gNfhsqc_CCLS, gNfhsqc_CCLS_U, gNhsqcTROSY_CCLS, gNhsqcTROSY_CCLS_U
SEA (Solvent-Exposed-Amides) sequences sea_gNfhsqc, sea_gCLNfhsqc, sea_gNhsqc, sea_gCLNhsqc, sea_gNtrosy, sea_gCLNtrosy
HADAMAC (HADamard-encoded AMino-ACid-type editing) hadamac
N15-HMQC gNhmqc  
N15-HMQC (very fast) sofastNhmqc, sofastNhmqcA  
N15-HMQC (very fast, Hadamard, VnmrJ 2.1B & up only) sofastNhmqcHT  
C13-HMQC (very fast, for kinetics) sofastCmhmqc  
N15-HMQCJ gNhmqcJ  
N15-HSQC gNhsqc, gNhsqcA  
N15-HSQC (Hadamard, VnmrJ 2.1B & up only) gNhsqcHT  
SOFAST N15-HSQC best_Nhsqc  
N15-HSQC with Homodecoupling gNhsqcHD, gNhsqcHDA  
N15-HSQC(IPAP) gNhsqc_IPAP, gNhsqc_IPAPA  
CPMG-N15-HSQC CPMGgNhsqc  
watergate N15-HSQC WGgNhsqc  
simultaneous N15/C13 HSCQ gNCm_hsqc, gNCm_trosyhsqc
N15-T1 (TROSY) gNT1  
N15-T2 (TROSY) gNT2  
N15-T1/T2 (TROSY) gNT1T2  
N15-NOE (TROSY) gNNOE  
N15-NOE gNnoe  
TROSY-Selected R1rho gNTSR1  
CRT-CPMG for NH gNcpmgex, gNcpmgex_NH  
N15-TOCSYHSQC gtocsyNhsqc, gtocsyNhsqcA  
N15-TOCSYHSQC (small molecules) gtocsyNhsqcSM  
N15-HSQCTOCSY gNhsqctocsy, gNhsqctocsyA  
N15-NOESYHSQC gnoesyNhsqc, gnoesyNhsqcA  
N15-NOESYHSQC (F1 13C,15N filtered) gnoesyNhsqc_CNfilt  
N15-NOESYHSQC (small molecules) gnoesyNhsqcSM  
N15-HSQCNOESY gNhsqcnoesy, gNhsqcnoesyA  
C13-HMQCNOESYHSQC(4D) gChmqcnoesyNhsqc, gChmqcnoesyNhsqcA  
N15-HMQCNOESYHSQC(4D) gNhmqcnoesyNhsqc  
N15-HSQCNOESYHSQC(3D) gNhsqcnoesyNhsqc3D  
N15-HSQCNOESYHSQC(4D) gNhsqcnoesyNhsqc, gNhsqcnoesyNhsqcA  
N15-HSQCTOCSYNOESYHSQC(4D) gNhsqctocsynoesyNhsqc, gNhsqctocsynoesyNhsqcA  
C13-NOESYHMQC gnoesyChmqc  
C13-NOESYHSQC gnoesyChsqc, gnoesyChsqcA  
Watergate C13-NOESYHSQC gnoesyChsqc_wg  
C13-NOESYHSQC (F1 13C,15N filtered) gnoesyChsqc_CNfilt  
C13-NOESYHSQC (small molecules) gnoesyChsqcSM  
C13-NOESYHSQC with SE gnoesyChsqcSE  
C13-HSQCNOESY gChsqcnoesy, gChsqcnoesyA  
C13-TOCSYHSQC gtocsyChsqc, gtocsyChsqcA  
C13-TOCSYHSQC (small molecules) gtocsyChsqcSM  
C13-TOCSYHSQC with SE gtocsyChsqcSE  
C13-HSQCTOCSY gChsqctocsy, gChsqctocsyA  
C13-ROESY-HSQC (small molecules) groesyChsqcSM  
N15-ROESY-HSQC (small molecules) groesyNhsqcSM  
N15,C13-NOESYHSQC gnoesyCNhsqc, gnoesyCNhsqcA  
C13-HMQC gChmqc  
C13-HMBC gChmbc  
CT-C13-HMQC CTgChmqc  
Fast 13C-HSQC gCfhsqc, gCfhsqcA  
C13-HSQC gChsqc, gChsqcP, gChsqcA  
2H pw90 calib ddec_pwxcal  
2H decoupling ddec_s2pul  
C(CO)NH (or C(CC-TOCSY-CO)N-NH ) gc_co_nh, gc_co_nhP, gc_co_nhA  
H(CCO)NH (or H(CC-TOCSY-CO)N-NH ) ghc_co_nh, ghc_co_nhP, ghc_co_nhA  
C13 TOCSY-NCH2 gc_tocsy_nch2A
amino acid side chain correl. gh2cnA
CBCA(CO)NH gcbca_co_nh, gcbca_co_nhP, gcbca_co_nhA  
CBCANH gcbca_nh, gcbca_nhP, gcbca_nhA  
HCACO ghca_co, ghca_coA  
HCACON ghca_co_n, ghca_co_nA  
HCACOCANH ghca_co_canh, ghca_co_canhA  
HNCO ghn_co, ghn_coP, ghn_coA  
SOFAST HNCO best_hncoP  
HNCO_JNH ghn_co_JNH, ghn_co_JNHA  
HNCO_NOE ghn_co_noe, ghn_co_noeA  
HNCO for JNH and JNCO couplings ghnco_DNCO_trosyA  
HNCOCO ghn_coco, ghn_cocoA  
HNHA ghnha  
HNHB ghnhb  
HNN ghnn, ghnnA  
HNCN ghcn, ghncnA  
LR-JCH gLRCH  
LR-JCC gLRCC  
HN(CO)HB ghn_co_hb, ghn_co_hbA  
HNCA ghn_ca, ghn_caP, ghn_caA  
SOFAST HNCA best_hncaP  
HCAN ghca_n  
CT-HNCA ghn_ca_CT, ghn_ca_CTA  
HNCACB ghn_cacb, ghn_cacbP, ghn_cacbA  
SOFAST HNCACB best_hncacbP  
CT-HNCACB ghn_cacbCTP  
HN(CA)CO ghn_ca_co, ghn_ca_coP, ghn_ca_coA, JIT_ghn_ca_coP  
SOFAST HN(CA)CO best_hncacoP  
HN(CO)CA ghn_co_ca, ghn_co_caP, ghn_co_caA  
SOFAST HN(CO)CA best_hncocaP  
HN(COCA)CB ghn_coca_cb, ghn_coca_cbA  
SOFAST HN(COCA)CB best_hncocacbP  
C-CH-TOCSY (projection reconstruction) cch_tocsyA  
HCCH-TOCSY hcch_tocsy, hcch_tocsyP, hcch_tocsyA  
HCCH-COSY hcch_cosy, hcch_cosyA  
DE-H(C)CH-TOCSY ghcch_tocsy  
3D/4D HCCH-TOCSY, HCa/HCb->Cmethyl ghcch_tocsy_cmhm*
aromatic proton-beta carbon correlation hbcbcgcdceheA, hbcbcgcdhdA  
13C obs. aliph.C-CO corr. cocaco_mqA, caco_sqapA, cocaco_sqA, cocaco_sqapA, cocaco_mqapA  
3D C(b),C(a)-CO-H(a) correlation hbcbcacocahaA  
3D C(a)-H(b)-H(a) correlation hacahbA  
3D HBHA(CO)NH ghbha_co_nh  
Intraresidue-only 3D HNCA ghnca_intraP  
SOFAST Intraresidue-only 3D HNCA best_ihncaP  
Intraresidue-only 3D HNCA ghnca_intraA (obsolete)
Intraresidue 3D HNCA (non-TROSY) ghnca_intra_nontrosyA (obsolete)
Intraresidue-only 3D HNCACB ghncacb_intraP  
SOFAST Intraresidue-only 3D HNCACB best_ihncacbP  
SOFAST Intraresidue-only 3D HNCACO best_ihncacoP  
Intraresidue-only 3D HNCACB ghncacb_intraA (obsolete)
Intraresidue 3D HNCACB (non-TROSY) ghncacb_intra_nontrosyA (obsolete)
(H)CACB_TOCSY_CmHm gcacb_tocsy_cmhmA, gcacb_tocsy_cmhm_sqA  
S3 N15-HSQC gNhsqcS3  
S3 ab-filtering for J(NH) gNtrosyS3  
NOESYHSQC 3D for heterodimers gnoesyChsqc_CC, gnoesyChsqc_NC, gnoesyNhsqc_NN, gnoesyNhsqc_CN  
S3 for J(N-CO)/(HN-CO) doublets ghn_Jnco_2DS3  
S3 J(NCa) in 1H-15N correlation ghn_Jnca_2DS3  
3D 1J(HaCa) and 2J(N(i)H(i)) ghnca_Jnha_3D  
S3 2D J(CoCa) in a 1H-15N correlation ghn_Jcoca_2DS3  
S3 3D J(N-CO) in 1H-15N-13CO correlation ghnco_Jnco_3DS3  
S3 3D 1J(NCa), 2J(NCa), 2J(HNCa) & 3J(HNCa) ghnco_Jnca_3DS3  
S3 3D 1J(COCa) & 3J(HNCa) ghnco_Jcoca_3DS3  
3D C(methyl-CT)-noesy-C(methyl-CT)-H(methyl) methylnoesyA  
4D 13C,15N edited NOESY with TROSY CN4Dnoesy_trosyA  
4D 15N,15N edited NOESY with TROSY NN4Dnoesy_trosyA  
3D HNCA with TROSY (deuterated) ghnca_trosy_3DA  
3D HN(CA)CB with TROSY (deuterated) ghncacb_trosy_3DA  
3D HN(CA)CO with TROSY (deuterated) ghncaco_trosy_3DA  
4D HN(CA)CO with TROSY (deuterated) ghncaco_trosy_4DA  
3D HNCO with TROSY (deuterated) ghnco_trosy_3DA  
3D HN(CO)CA_SEQ with TROSY (deuterated) ghncoca_seq_trosy_3DA  
4D HN(CO)CA_SEQ with TROSY (deuterated) ghncoca_seq_trosy_4DA  
4D HN(CO)CA_SIM with TROSY (deuterated) ghncoca_sim_trosy_4DA  
3D HN(CO)(CA)CB with TROSY (deuterated) ghncocacb_trosy_3DA  
References are given in manual files and psglib codes.
Many sequences have a TROSY option, with gradient selection.
Sequences marked "deuterated" should only be used on fully deuterated proteins (no proton decoupling used).

SpinCAD Pulse Sequences for Proteins:

Common Name Sequence Name(s)
N15-HSQC gNhsqcSP  
C(CO)NH (or C(CC-TOCSY-CO)N-NH) gc_co_nhSP  
CBCA(CO)NH gcbca_co_nhSP  
CBCANH gcbca_nhSP  
H(CCO)NH (or H(CC-TOCSY-CON-NH) ghc_co_nhSP  
DE-H(C)CH-TOCSY ghcch_tocsySP  
HCCHTOCSY hcch_tocsySP  
HNCA ghn_caSP  
HN(CA)CO ghn_ca_coSP  
HNCACB ghn_cacbSP  
HNCO ghn_coSP  
HN(CO)CA ghn_co_caSP  
These have been written to provide the same features as the above equivalents.

Pulse Sequences optimized for Polynucleotides:

Common Name Sequence Name(s)
1H PRESAT, WET, jump-return, watergate rna_water  
1H PRESAT-NOESY rna_tnnoesy  
1H PRESAT-DQCOSY rna_tndqcosy  
1H WET-ROESY rna_wroesy  
1H WATERGATE-ROESY rna_wroesy  
1H WATERGATE-NOESY rna_WGnoesy  
1H WET-NOESY rna_wetnoesy  
1H WET-TOCSY rna_wettntocsy  
1H SS-NOESY rna_SSnoesy  
1H 1-1 echo NOESY rna_11noesy  
13C HSQC rna_gChsqc, rna_gChsqcA  
13C TROSY rna_gCtrosy, rna_gCtrosyA  
2D HSQC, C13 homodec & Base Filtering rna_gChsqc_CCdec
3D NOESY-HSQC, C13 homodec. & Base Filtering rna_gnoesyChsqc_CCdec
3D TOCSY, F1 ribose carbons, F2 C1' rna_cchtocsy_CCdec
3D CCHCOSY, F1 ribose arbons, F2 C1' rna_cchcosy_CCdec
15N HSQC rna_gNhsqc, rna_gNhsqcA  
15N TROSY rna_WGgNtrosy  
13C HMQC rna_gChmqc  
13C HMQC-TOCSY rna_hmqc_tocsy  
13C CT-HMQC rna_CTgChmqc, rna_CTgChqmcA  
15N HMQC rna_gNhmqc  
15N WG-HSQC rna_WGgNhsqc  
15N HSQC(long-range) rna_WGgNhsqc  
15N CPMG-HSQC rna_CPMGgNhsqc  
13C NOESY-HSQC rna_gnoesyChsqc, rna_gnoesyChsqcA  
15N NOESY-HSQC rna_gnoesyNhsqc, rna_gnoesyNhsqcA  
gd-HCCH-TOCSY rna_hcch_tocsy  
DE-H(C)CH-TOCSY rna_ghcch_tocsy  
HCCH-COSY rna_hcch_cosy, rna_hcch_cosyA  
HCCH-RELAY rna_hcch_cosy, rna_hcch_cosyA  
CPMG-NOESY rna_CPMG_noesy  
HCN rna_HCN  
HCP rna_HCP  
HP-COSY rna_HPcosyHCP  
C-HNCCCH rna_CUhnccch  
U-HNCCCH rna_CUhnccch  
3D (H6/H5)C6/C5(C4)NH with CPMG rna_CUhnccch_CCdec
A-HNC-TOCSY-CH rna_Ahncch  
A-HCCH-TOCSY rna_hcch_tocsy  
G-HNC-TOCSY-CH rna_Ghncch  
HNN-COSY rna_HNNcosy, rna_HNNcosyA, rna_fHNNcosyA  

All of these can be run at any field strength after just calibrating the 90's for 1H, 13C and 15N. All power levels are automatically set for proper excitation. 2H decoupling is often available as an option by setting dm3='nyn' (and setting proper values for channel 4 decoupling parameters). Operation is valid only for UNITYplus and UNITY INOVA.

All r.f. events including pulses, spinlocks and decoupling are automatically created for all field strengths by autocalibrate/autoupdate for all sequences. Power levels for each of these are then set by the pulse sequence itself, not the operator, based on the high-power pw, pwC and pwN calibrations. Optional power limits are available if the global parameter BPcryogenic=1. In this case, decoupling power levels are checked and waveforms made appropriately during the autocalibrate/autoupdate processes. These power limits are displayed in the "Decoupling" Tcl-dg panel (VNMR) and in the BioPack "Options" page (VnmrJ) within the ghn_co Acquire pages.

All experiments in which CH protons are the relevant originating magnetizations or are the detected magnetization can be skipped for the case of fully-deuterated proteins (for automatic calibration or automatic 2D).

Two alternative methods of using phase-ramped pulses are included. These methods call Pbox for shape creation at the time of dps and go. No shapes are required in shapelib for this method. These sequences have a "P" or "A" appended to the normal names. The former must be compiled the bionmr.h include file, while the latter require the Pbox_bio.h and Pbox_psg.h include files (C pulse sequences only).

The "P" versions use new psg elements which are written with protein 13C bandwidths pre-defined so that terms such as "ca", "co" and "cacb" are used. See the file BioPack.bionmr in ~/vnmrsys/manual or in /vnmr/manual/ for details. The operation, parameters and performance of these is at least as good as the standard BioPack sequences. The only differences are that the phi7cal value will be different, and that the dof value is always set to the carbonyl carbon frequency for all experiments (contributed by Boban John, Varian, and Robin Bendall).

The "A" versions include a header section of the pulse sequence in which all shapes are created and parameter values from these shapes are obtained at go time. This mode of operation allows conversion of existing pulse sequences to BioPack versions without modification of the underlying codes (contributed by Eriks Kupce, Varian, Sept. 2002). See the file BioPack.Asequences in ~/vnmrsys/manual or in /vnmr/manual for details on this approach, and how to convert an existing non-BioPack sequence to a BioPack version.

All of the above sequences are compiled during installation.