IU NMR Facility

The variable temperature function is resumed on all the spectrometers.

Variable temperature function on the I500, I400, and Gem300 is temporarily unavailable due to house nitrogen outage, probably until tomorrow morning.

The 800 and 600 have been added to the “view current activity” list on the main MagRes page. Please note that currently only the most commonly used parameters are taken into account in experiment time calculation, thus the experiment time displayed may be inaccurate for BioPack.

We just installed a new UPS. The I500 is back running now.

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:
——————————————-

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:
———————————
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
—————————————–
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

—————–end————-

A new UPS was ordered for the I500. It’s down until we get and install the UPS, which should be next week.

You can email .fid data files from spectrometers or workstations within VnmrJ using the command “vnmremail(‘filename’,’email address’)”. For example “vnmremail(‘/home/doebrown/test.fid’,’doebrown@indiana.edu’).

The files are compressed and archived into .tgz format (tar + gzip) so you’ll need an archiving utility program on your mac or PC to retrieve the data. In the example above test.fid will be sent as test.fid.tgz attachment.

PeaZip is recommended for the PC. PeaZip makes retrieval straightforward but you may have to do it in 2 steps, which are effectively gunzip to a .tar file then “untar”.

We’re working on an easier to use method but vnmremail will do the job for now.

The UPS power supply for the I500 was failed during this weekend and is now being repaired. The I500 is unavailable until the UPS get fixed.

As we know, array in VnmrJ can be used to optimize parameters for data
collection and to acquire a series of dataset, which are not limited to 1D
only. For example, for backbone dynamics measurement, 15N R1, R2,
heteronuclear NOE, one can use array to collect all the individual 2D HSQC
type data in an interleaved fashion, rather than to collect one by one.
There are advantages to use array here. First, system conditions such as lock
level, temperature etc, are averaged over entire datasets. Second, the
experiment can be stopped before it is fully completed and the data is still
usable. If without array, system conditions could be a little different from
one delay point to another. Also, one has to wait till the acquisition of the last delay point
finishes in order to process the data. Obviously, it is more
convenient to use array.

To set up such arrayed 2D NMR is not difficult. Below is an example used
to acquire 15N R1 relaxation data. Just 4 more commands and you are ready
to go.

/* setup a regular HSQC,  choose N15T1  */

relaxT=0.02,0.05,0.1,0.2,0.4,0.6,0.9,1.3    /*8 delays in relaxT array */
array=’relaxT,phase’       /* keep phase the innermost loop */
bs=1                       /* block size */
il=’y’                     /* interleave on for dynamics experiment */

go                         /* collect data */

Below is an example to monitor HD exchange using HSQC. ‘pad’ is arrayed.
In the example, 4 hsqc is acquired with 10 min delay in between.

/* for a series of HSQC, eg. to monitor HD exchange, try array ‘pad’ */

il=’n’                     /* no interleave for HD exchange HSQC*/
pad=0.5,600,600,600        /*pre-acquisition delay in sec, 4 HSQC */

/* the following array will collect 99 HSQC continuously */

array(‘pad’,99,1.0,0.0)

array=’pad,phase’          /* keep phase the innermost loop */

The arrayed data has a single fid file and can’t be processed within VnmrJ.
The attached nmrPipe scripts can process the data.

######### Beginning of fid.com #########
#!/bin/csh

var2pipe -in ./fid \
-noaswap  \
-xN              1024  -yN  8      -zN               128  \
-xT               512  -yT  8      -zT                64  \
-xMODE        Complex  -yMODE Real -zMODE       Rance-Kay \
-xSW         7225.434  -ySW 0      -zSW         1823.306  \
-xOBS         599.801  -yOBS 0     -zOBS          60.784  \
-xCAR           4.773  -yCAR 0     -zCAR         120.134  \
-xLAB              HN  -yLAB ID     -zLAB            N15  \
-ndim               3  -aq2D          States  \
| nmrPipe -fn TP \
| nmrPipe -fn ZTP \
| nmrPipe -fn TP -hyper \
| pipe2xyz -out ./data/test%03d.fid -verb -ov

sleep 5
######### End of fid.com #########

######### Beginning of nmrproc.com #########
#!/bin/csh
xyz2pipe -in data/test%03d.fid -x \
# SOL and POLY similar result \
| nmrPipe -fn SOL                                        \
| nmrPipe -fn GM  -g1 5.0 -g2 10.0 -g3 0.0 -c 0.5        \
| nmrPipe  -fn ZF -size 2048                             \
| nmrPipe  -fn FT -auto                                  \
| nmrPipe  -fn PS -p0 136.00 -p1 0.00 -di -verb          \
| nmrPipe  -fn EXT -x1 6.5ppm -xn 10.5ppm -sw             \
| nmrPipe  -fn TP                                        \
| nmrPipe -fn LP  -ps90-180 -ord 8                       \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5       \
| nmrPipe  -fn ZF -size 256                              \
| nmrPipe  -fn FT -auto                                  \
| nmrPipe  -fn PS -p0 0.00 -p1 0.00 -di -verb          \
| nmrPipe  -fn TP                 \
| pipe2xyz -out ft/test%03d.ft2 -x
######### End of nmrproc.com #########

… to the new Indiana University NMR website and blog.