List of BioPack experiments on the Inova 600

Description of BioPack experiments

This is a list supplied by Varian that translates descriptions of the experiments available in BioPack into sequence names. At the end, the differences between standard, "A," and "P" sequences are explained. This list is current with the 12/15/07 release of BioPack. In addition to the credits shown below for the original contributions, George Gray has been maintaining BioPack and packaging the updates for some years, and Rolf Kyburz maintains Varian's software archives and edits the weekly Varian software/applications newsletter.

BioPack is the result of the merging of ProteinPack and RnaPack.
ProteinPack: originally contributed by Robin Bendall (Melbourne)
RnaPack: originally contributed by Peter Lukavsky (Stanford)
Automated Shape Creation: contributed by Eriks Kupce (Varian)
SpinCAD pulse sequences for proteins contributed by Robin Bendall.

BioPack also incorporates the use of "probe files" as is customary in VNMR/VnmrJ Chempack. This means that calibrations are stored in probe files rather than in parameter sets. Experiment setup macros (e.g. ghn_co) and the BPrtppar macro include retrievals from the active probe file for calibrations of all types.

Should you want to update BioPack to a newer version in the future, you may not need to download and install an entire new BioPack - if your basic installation is not too old, installing "psglib/BPupdate" may be sufficient.

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`
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.c, gNCm_trosyhsqc.c`
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`
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*.c`
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`
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, 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.