BioPack consists of pulse sequences used mainly for proteins and nucleic acids. It is updated constantly. New sequences will be added whenever new version of VnmrJ is released. As in VnmrJ version 2.3A, there are >360 sequences available. If you ever wonder what they are, below is a list.
The pulse sequences comprising BioPack are:
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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 Diff. 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 HNCO for C=O labeled proteins gNfhsqc_CCLS, gNfhsqc_CCLS_U,
Fast HNCO for C=O labeled proteins gNhsqcTROSY_CCLS, gNhsqcTROSY_CCLS_U
SEA (Solvent-Exposed-Amides) seq. sea_gNfhsqc, sea_gCLNfhsqc,
SEA (Solvent-Exposed-Amides) seq. sea_gNhsqc, sea_gCLNhsqc,
SEA (Solvent-Exposed-Amides) seq. sea_gNtrosy, sea_gCLNtrosy
HADAMAC (HADamard-encoded AMino-ACid-type editing) hadamac.c
N15-HMQC gNhmqc
N15-HMQC (very fast) sofastNhmqc, sofastNhmqcA
N15-HMQC (very fast, Hadamard) sofastNhmqcHT (VnmrJ 2.1B & up only)
C13-HMQC (very fast, for kinetics) sofastCmhmqc
N15-HMQCJ gNhmqcJ
N15-HSQC gNhsqc, gNhsqcA, gNhsqcHT
SOFAST N15-HSQC best_Nhsqc
N15-HSQC (Hadamard) gNhsqcHT (VnmrJ 2.1B & up only)
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
13C,15N-F1 filtered gnoesyNhsqc gCNfilnoesyNhsqcA
N15-NOESYHSQC (F1 13C,15N filt.) 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 filt.) 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
N15,C13-NOESYHSQC gnoesyCNhsqc, gnoesyCNhsqcA
C13-ROESY-HSQC (small molecules) groesyChsqcSM
N15-ROESY-HSQC (small molecules) groesyNhsqcSM
C13-HMQC gChmqc
C13-HMBC gChmbc
Clean HMBC cleanHMBC
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
CT-HNCA ghn_ca_CT, ghn_ca_CTA
HCAN ghca_n
HNCACB ghn_cacb, ghn_cacbP, ghn_cacbA
SOFAST HNCACB best_hncacbP
CT-HNCACB ghn_cacbCTP
HN(CO)CA ghn_co_ca, ghn_co_caP, ghn_co_caA
SOFAST HN(CO)CA best_hncocaP
HN(CA)CO ghn_ca_co, ghn_ca_coP, ghn_ca_coA,
JIT_ghn_ca_coP
SOFAST HN(CA)CO best_hncacoP
HN(COCA)CB ghn_coca_cb, ghn_coca_cbA
SOFAST HN(COCA)CB best_hncocacbP
C-CH-TOCSY (projection reconstr.) 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 corr. hbcbcgcdceheA, hbcbcgcdhdA
13C obs. aliph.C-CO corr. cocaco_mqA, caco_sqapA, cocaco_sqA,
cocaco_sqapA cocaco_mqapA
3D C(a)-H(b)-H(a) corr. hacahbA
3D C(b),C(a)-CO-H(a) corr. hbcbcacocahaA
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
13C,15N-F1 filtered noesyChsqc gCNfilnoesyChsqcA
13C,15N-F1 filtered noesyChsqcSE gCNfilnoesyChsqcSE
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
Cross-corr. relax. NH DD / 15N CSA sSCT_CCR
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 w/ TROSY (deuterated) ghncacb_trosy_3DA
3D HN(CA)CO w/ TROSY (deuterated) ghncaco_trosy_3DA
4D HN(CA)CO w/ TROSY (deuterated) ghncaco_trosy_4DA
3D HNCO with TROSY (deuterated) ghnco_trosy_3DA
3D HN(CO)CA_SEQ w/TROSY (deuter.) ghncoca_seq_trosy_3DA
4D HN(CO)CA_SEQ w/TROSY (deuter.) ghncoca_seq_trosy_4DA
4D HN(CO)CA_SIM w/TROSY (deuter.) ghncoca_sim_trosy_4DA
3D HN(CO)(CA)CB w/TROSY (deuter.) ghncocacb_trosy_3DA
3D HNCACB, non-linear sampling ghn_cacbNLS
3D HN(CA)CO, non-linear sampling ghn_ca_coNLS
3D HNCA, non-linear sampling ghn_caNLS
3D HN(COCA)CB, non-linear sampling ghn_coca_cbNLS
3D HNCOCA, non-linear sampling ghn_co_caNLS
3D HNCO, non-linear sampling ghn_coNLS
6D PR HC(CO)NH ghc_co_nh_6dA
(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 experiments for proteins:
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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)
EXPERIMENTS optimized for polynucleotides
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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 Filt. rna_gChsqc_CCdec
3D NOESY-HSQC, C13 HD & Base Filt. rna_gnoesyChsqc_CCdec
3D TOCSY, F1 ribose C, F2 C1′ rna_cchtocsy_CCdec
3D CCHCOSY, F1 ribose C, 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
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