1. Examples of 2D and 3D spectra
Processing NUS Data
Examples of 2D and 3D spectra
4D to be appended soon.
Assumed knowledge: NMRPipe and NMRDraw
: Unix Environment

2. 2D Processing 1D Reconstruction
15N, 13C HSQC and Homonuclear Spectra
Single indirect dimension acquired non- uniformly
We convert data from Bruker/Varian like normal
Processing starts by doing FT on directly acquired data first
Data is then transposed... ready for reconstruction

3. 2D Spectra Conversion fid.com
bruk2pipe -in ser -DMX -swap -decim 24 -dspfvs 12 \
#!/bin/sh -f
-xN yN \
-xT yT \
-xMODE DQD -yMODE Echo-AntiEcho \
-xSW ySW \
-xOBS yOBS \
-xCAR yCAR \
-xLAB H -yLAB N \
-ndim aq2D States \
-out data.fid -ov -verb
Nothing Special for 2D Spectra Conversion!

4. Direct Dimension Transform ft1.com
nmrPipe -in data.fid \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.3 -end pow 2 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT \
| nmrPipe -fn PS -p0 46 -p di \
| nmrPipe -fn EXT -left -sw -verb \
| nmrPipe -fn TP \
-verb -ov -out test.ft1
Viewing this output in NMRPipe allows you to phase direct dimension.

5. Direct Dimension Processing Only

6. Let’s fill in the blanks ist.com
#!/bin/csh
istHMS -in $1 -out $2 -zero 1 -vlist sched.1d \
-xN 440 -over 0 -ref 0 -itr 400 -verb 1
If this script is called ist.com then you would run it as:
ist.com test.ft1 test.ft2

7. Direct Dimension Processing Only

8. Let’s FT indirect dimension! ft2.com
nmrPipe -in test.ft2 \
| nmrPipe -fn SP -off 0.3 -end pow 1 -size c \
| nmrPipe -fn ZF -size \
| nmrPipe -fn FT \
| nmrPipe -fn PS -p0 90 -p di \
| nmrPipe -fn POLY -ord 0 -auto \
| nmrPipe -fn TP \
-verb -ov -out test.ft3
pipe2ucsf test.ft3 HSQC.ucsf

9. 2D Processing Done

10. Simplified 2D Reconstruction ft12.com
nmrPipe -in data.fid \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.5 -end size 512 -c 1.0 \
| nmrPipe -fn ZF -size 1024 \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p p di \
| nmrPipe -fn EXT -left -sw -verb \
| nmrPipe -fn TP \
| istHMS -xN 512 -sched ./sched.1d -itr 400 \
| nmrPipe -fn SP -off 0.5 -end c size 512 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn PS -p p di -verb \
| nmrPipe -fn POLY -ord 0 -auto \
-ov -out test.ft12

11. Looks great!

12. 3D Processing 2D Reconstruction
Triple Rez, 3D NOESY, HC(C)H, XX(CO)NH etc
Two indirect dimensions acquired non-uniformly
We convert data from Bruker/Varian differently and cautiously
Processing starts by doing FT on directly acquired data first - just like 2D
Data is then transposed... ready for reconstruction
Reconstruction followed by FT in 2nd and 3rd dimension.

13. 3D Spectra Conversion fid.com
bruk2pipe -in ./ser \
#!/bin/csh
-bad 0.0 -noaswap -DMX -decim 24 -dspfvs 12 -grpdly 0 \
-xN yN zN \
-xT yT zT \
-xMODE DQD -yMODE Real -zMODE Real \
-xSW ySW zSW \
-xOBS yOBS zOBS \
-xCAR yCAR zCAR \
-xLAB HN -yLAB N -zLAB C \
-ndim aq2D States \
| nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr \
| pipe2xyz -out ./fid/test%03d.fid -verb -ov -to 0
What is going on here?

14. What is going on here? Data no longer collected as a series of planes.
Instead, treat data as string of points acquired according to the schedule.
In 3D spectrum there are 4 FIDs per indirect point. -yN = 4
2 FIDs for each indirect dimension.
E.g. 2 FIDs for Nitrogen (a complex point)
2 FIDs for Carbon (a complex point)
This is how the Pulse Program Acquires the data
Then there are 818 points acquired. -zN = 818
We treat each FID is real for conversion
Each FID is put into a complex line of data by the reconstruction program
Any dimension with non-complex acquisition (read Echo-AntiEcho) needs to be labeled as such.
| nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr \
Here the Y dimension (Nitrogen) is labeled as Rance-Kay (Echo-AntiEcho).

15. Direct Dimension Transform ft1xyz.com
xyz2pipe -in fid/test%03d.fid -x \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.3 -end pow 2 -c 1.0 -size 512 \
| nmrPipe -fn ZF -size \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p p di \
| nmrPipe -fn EXT -x1 11.0ppm -xn 5.5ppm -sw \
| pipe2xyz -ov -out xyz/test%03d.ft1 -x
Read in x dimension, write out to x dimension
This allows phasing of direct dimension in NMRPipe.

16. Direct Dimension Processing Only

17. Phase, Transpose for Reconstruction ft1.com
xyz2pipe -in fid/test%03d.fid -x \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.3 -end pow 2 -c 1.0 -size 512 \
| nmrPipe -fn ZF -size \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p p di \
| nmrPipe -fn EXT -x1 11.0ppm -xn 5.5ppm -sw \
| pipe2xyz -ov -out xyz/test%03d.ft1 -z
Read in x dimension, write out to z dimension
This places indirect data in the x and y dimensions.
This is necessary for istHMS reconstruction.

18. Fill in with Blanks, Reconstruct ist.csh
set F = $1
#!/bin/csh -xv
set in = $F:t
set out = $F:t:r.phf
set ft1 = $F:t:r.ft1
echo $in $out $ft1
istHMS -dim 2 -incr 1 -xN 64 -yN 128 -user 1 \
-itr 400 -verb 1 -ref 0 -vlist ./sched.2d \
< ./yzx/${in} >! ./yzx_ist/${out}
-xN and -yN can be replaced with -autoN which gets the limits of reconstruction from the schedule file
Each file in ‘yzx’ directory needs to be processed this way.
Opportunity for parallelization of this process.

19. Cluster Submission E.g. foreach F (yzx/test*.ft1)
qsub -cwd ./ist.csh $F
end
Many other methods. Consult your sys/cluster admin.

20. Multicore Laptop/Desktop Processing
Use a perl program that will run multiple jobs for you at once, but never more than one job per possible thread.
My Macbook pro: 4 cores, 8 threads. 8 processes at once. Not too shabby.
parallel -j 100% 'csh ist.csh {} 2> /dev/null; echo {}' ::: yzx/test*.ft1
Running at 100% will make things toasty. You can run at 50% etc etc.
This will take minutes for typical spectra....
coffee time!

21. Reordering FIDs phf2pipe.com
#!/bin/csh
xyz2pipe -in yzx_ist/test%03d.phf \
| phf2pipe -user 1 -xproj xz.ft1 -yproj yz.ft1 \
| pipe2xyz -out rec/test%03d.ft1
FIDs are fully reconstructed from last step
FIDs are now in conventional order (planes)
xproj and yproj give the first plane in each indirect dimension - for phasing.
Lets look at yz.ft1

22. Projection Phasing

23. Final Processing ft23.com
#!/bin/csh -f
xyz2pipe -in rec/test%03d.ft1 -x \
| nmrPipe -fn SP -off 0.5 -end pow 2 -c 0.5 \
| nmrPipe -fn ZF -size \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p p di \
| nmrPipe -fn REV -verb \
| nmrPipe -fn TP \
| nmrPipe -fn ZF -size \
| nmrPipe -fn FT -alt -verb \
| nmrPipe -fn PS -p p di \
| nmrPipe -fn ZTP \
> rec/data.pipe
pipe2xyz -in rec/data.pipe -out rec/test%03d.ft3 -y
pipe2ucsf rec/data.pipe GB1_NUS_HNCO.ucsf

24. Nice Spectrum!