3D TROSY NOESY

Ref.:
A.Meissner, and O.W.Sørensen J.Magn.Reson. 142, 195-198 (2000). (Three-Dimensional Protein NMR TROSY-Type ¹⁵N-resolved ¹H^N-¹H^N NOESY Spectra with Diagonal Peak Suppression)

T.Schulte-Herbrüggen, and O.W.Sørensen J.Magn.Reson. 144, 123-128 (2000). (Clean TROSY: compensation for relaxation-induced artefacts)

Delays:  = (2J_NH)^-1; _I = (2J_NH)^-1 - _I; = gradient delay; _m = NOESY mixing time.

Phases for Varian Unity Inova:   = -y; " =  + ; {_I = y; _S = y - _S } echo (t₁ - t₂), {_I = -y; _S = -y - _S } antiecho (t₁ - t₂);

Phases for Bruker DRX:   = y; " =  + ; {_I = -y; _S = -y - _S } echo (t₁ - t₂), {_I = y; _S = y - _S } antiecho (t₁ - t₂);

The uncompensated TROSY experiment employs _S = _I = 0.

For all odd-numbered scans the phase  is x and the left dashed  pulse on the S channel is applied whilst for all even-numbered scans  is y and the right dashed  pulse on the S channel is applied with opposite receiver phase.

Two data sets: A: { = 0, ; receiver = 0, } and B: {  = /2, 3/2; receiver /2, 3/2} both for echo(e) and antiecho(a) between t₁ and t₂ are recorded. {A(a) - B(a)}, {A(e) + B(e)}, {A(e) - B(e)}, and {A(a) + B(a)} yield the four pathways {S^-,S⁺}(t₁) -> {I^-, I⁺}(t₂).

diag  y:      without diagonal peak suppression
      n:      with diagonal peak suppression (default)

sub   a:      subspectrum a (for weighted combination with b)
      b:      subspectrum b
      n:      online 1:1 combination of a and b (default)

SW2 can be reduced when a pre-processing TPPI-type offset shift is applied. For folding the water resonance to the edge of the spectrum set SW2 = 0.5*SW.

To generate a selective water pulse shape, copy water_sc.inp to your $HOME/vnmrsys/shapelib directory, adjust ref_pwr and ref_pw90 according to your proton pulse calibration and type the command: Pbox -f water_sc.inp

An output like
>>> Set pulse width to 1.0000 ms <<<
>>> Set pulse power to 21 dB <<<
appears.

Remember to change the parameters pwater (pulse width in us) and pwaterlvl (pulse power).

Processing of 3D TROSY NOESY:

Combination of data set recorded with array = 'phase2,phase'

• change into the directory where the dataset is located
• run the dataset combination routine >tr_no_combine "original name" "new name" "ni" "ni2" "np" n "wf" "O2_shift" "SW2" "initial t₂"<

(e.g. tr_no_combine protein_1 protein_1_ea 32 512 2048 n 1.0  2500 5000 0.0)
the subroutines tr_no_sort and shift_o2 will be called. Notice, that the dataset names are given without the .fid extention. protein_1 referes to the directory protein_1.fid.
For data recorded with array = 'phase2,phase,sub' the sub flag must be set to y  (tr_no_combine protein_1 protein_1_ea 32 512 2048 y 1.0  2500 5000 0.0)
• use your usual software for processing and phase correction. The data set is now echo / antiecho in both indirect dimensions.

Note: processing with Xwinnmr:
1. vconv on program versions older than 2.6 does not work properly with this type of data
2. indirect dimensions will be interchanged t₁ -> F₂ and t₂ -> F₁
3. When using array = 'phase2,phase,sub' the parameter file (procpar) must be edited before invoking vconv. Change the line after the array entry

array 2 2 256 0 0 2 1 1 1 64
1 "phase2,phase,sub" to 1 "phase2,phase"

tr_no_sort.c / tr_cno_sort.c installation:
change to the directory with the tr_no_sort.c file
type cc tr_no_sort.c -o $HOME/bin/tr_no_sort
and cc tr_cno_sort.c -o $HOME/bin/tr_cno_sort
this will compile the programs and save the executable files in the $HOME/bin directory. Make sure the directory exists or choose another location. Make also sure your PATH environment variable contains the directory you are using.

Content
Pulse sequence:        trosy_noesy.c
Parameters:            trosy_noesy.par
Pbox input file:       water_sc.inp

Pre-processing script: tr_no_combine
Sorting routine:       tr_no_sort.c
                       tr_cno_sort.c
O2_shift routine:      shift_o2.c
 

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Place gradient files trEA_1 (Gradient G₁), trEA_2 (Gradient G₂), and trEA_3 (Gradient G₃) in the /u/exp/stan/nmr/lists/gp directory. (To change the ratio of the shaded gradients, these files can be edited. The two entries represent the relative strength for echo and antiecho, respectively). The gradient strengths are set within ased.

Processing of 3D TROSY NOESY:

• run pre-processing au program for dataset combination by typing tr_no_combine (if not compiled yet call the program with the xau tr_no_combine command. The au program will call the tr_no_br routine, make sure it is installed as described below)
• Determine phase correction in F₃ from 2D plane (2-3) and add 180 to PHC0 value, and correction in F₁ from the 1-3 plane. Phase correction in F₂: PHC0 = 90 PHC1 = 0.
• start 3D processing under consideration of Bug #2435 from Bruker Bug Database. (Apply the 'c' option with the tf3 command and choose equal 'xdim' values in F₂ and F₁)

tr_no_br.c installation:
change to the directory with the tr_no_br.c file
type cc tr_no_br.c -o $HOME/bin/tr_no_br
this will compile the programs and save the executable files in the $HOME/bin directory. Make sure the directory exists or choose another location. Make also sure your PATH environment variable contains the directory you are using.

Content
Pulse sequence:            trosy_noesy
Gradient files:           trEA_1
                          trEA_2
                          trEA_3

au pre-processing script: tr_no_combine
Sorting routine:          tr_no_br.c
 

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