assign

BioPack Pulse Sequences for Proteins:

Common Name	Sequence Name(s)
PRESAT - includes PRESAT, WET, shaped-pulse PRESAT, jump-return, watergate (soft, 3919, W5)	`water`
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`
N15-HMQC	`gNhmqc`
N15-HMQCJ	`gNhmqcJ`
N15-HSQC	`gNhsqc, gNhsqcA`
N15-HSQC with Homodecoupling	`gNhsqcHD, gNhsqcHDA`
N15-HSQC(IPAP)	`gNhsqc_IPAP, gNhsqc_IPAPA`
CPMG-N15-HSQC	`CPMGgNhsqc`
watergate N15-HSQC	`WGgNhsqc`
N15-T1 (TROSY)	`gNT1`
N15-T2 (TROSY)	`gNT2`
N15-NOE (TROSY)	`gNNOE`
N15-NOE	`gNnoe`
CRT-CPMG for NH	`gNcpmgex`
N15-TOCSYHSQC	`gtocsyNhsqc, gtocsyNhsqcA`
N15-HSQCTOCSY	`gNhsqctocsy, gNhsqctocsyA`
N15-NOESYHSQC	`gnoesyNhsqc, gnoesyNhsqcA`
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-NOESYHSQC	`gnoesyChsqc, gnoesyChsqcA`
C13-NOESYHSQC with SE	`gnoesyChsqcSE`
C13-HSQCNOESY	`gChsqcnoesy, gChsqcnoesyA`
C13-TOCSYHSQC	`gtocsyChsqc, gtocsyChsqcA`
C13-HSQCTOCSY	`gChsqctocsy, gChsqctocsyA`
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`
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`
HNCO_JNH	`ghn_co_JNH, ghn_co_JNHA`
HNCO_NOE	`ghn_co_noe, ghn_co_noeA`
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`
HCAN	`ghca_n`
CT-HNCA	`ghn_ca_CT, ghn_ca_CTA`
HNCACB	`ghn_cacb, ghn_cacbP, ghn_cacbA`
CT-HNCACB	`ghn_cacbCTP`
HN(CO)CA	`ghn_co_ca, ghn_co_caP, ghn_co_caA`
HN(CA)CO	`ghn_ca_co, ghn_ca_coP, ghn)ca_coA`
HN(COCA)CB	`ghn_coca_cb, ghn_coca_cbA`
C-CH-TOCSY	`cch_tocsyA`
HCCH-TOCSY	`hcch_tocsy, hcch_tocsyP, hcch_tocsyA`
HCCH-COSY	`hcch_cosy, hcch_cosyA`
DE-H(C)CH-TOCSY	`ghcch_tocsy`
aromatic proton-beta carbon correlation	`hbcbcgcdceheA, hbcbcgcdhdA`
3D C(a)-H(b)-H(a) correlation	`hacahbA`
3D C(b),C(a)-CO-H(a) correlation	`hbcbcacocahaA`
3D HBHA(CO)NH	`ghbha_co_nh`
Intraresidue-only 3D HNCA	`ghnca_intraA`
Intraresidue-only 3D HNCACB	`ghncacb_intraA`
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.c`
3D HN(CA)CB with TROSY (deuterated)	`ghncacb_trosy_3DA.c`
3D HN(CA)CO with TROSY (deuterated)	`ghncaco_trosy_3DA.c`
4D HN(CA)CO with TROSY (deuterated)	`ghncaco_trosy_4DA.c`
3D HNCO with TROSY (deuterated)	`ghnco_trosy_3DA.c`
3D HN(CO)CA_SEQ with TROSY (deuterated)	`ghncoca_seq_trosy_3DA.c`
4D HN(CO)CA_SEQ with TROSY (deuterated)	`ghncoca_seq_trosy_4DA.c`
4D HN(CO)CA_SIM with TROSY (deuterated)	`ghncoca_sim_trosy_4DA.c`
3D HN(CO)(CA)CB with TROSY (deuterated)	`ghncocacb_trosy_3DA.c`
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`
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`
A-HNC-TOCSY-CH	`rna_Ahncch`
A-HCCH-TOCSY	`rna_hcch_tocsy`
G-HNC-TOCSY-CH	`rna_Ghncch`
HNN-COSY	`rna_HNNcosy, rna_HNNcosyA`

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.

These sequences are compiled during the installation.