Processing NUS
Data
Examples of 2D and 3D spectra
4D to be appended soon.
Assumed knowledge: NMRPipe and NMRDraw
: Unix Environment
2D Processing
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1D Reconstruction
15N, 13C
HSQC and Homonuclear
Spectra
• Single indirect dimension acquired nonuniformly
• We convert data from Bruker/Varian like
normal
• Processing starts by doing FT on
directly acquired data first
• Data is then transposed... ready for
2D Spectra Conversion
fid.com
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#!/bin/sh -f
bruk2pipe -in ser -DMX -swap -decim 24 -dspfvs 12 \
-xN
2048
-yN
80
\
-xT
1024
-yT
40
\
-xMODE
DQD
-yMODE
Echo-AntiEcho
-xSW
7002.801
-ySW
1824.568
\
-xOBS
500.130
-yOBS
50.678
\
-xCAR
4.697
-yCAR
118.000
\
-xLAB
1H
-yLAB
15N
\
-ndim
2
-aq2D
States
\
-out data.fid -ov -verb
\
• Nothing Special for 2D Spectra Conversion!
Direct Dimension Transform
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ft1.com
nmrPipe -in data.fid \
| nmrPipe -fn SOL
\
| nmrPipe -fn SP -off 0.3 -end 0.98 -pow 2 \
| nmrPipe -fn ZF -auto
\
| nmrPipe -fn FT
\
| nmrPipe -fn PS -p0 46 -p1 0.0 -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.
Direct Dimension Processing Only
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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
Direct Dimension Processing Only
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Let’s FT indirect
dimension!
ft2.com
nmrPipe -in test.ft2 \
| nmrPipe -fn SP -off 0.3 -end 0.98 -pow 1 -size 512 -c 0.5
| nmrPipe -fn ZF -size 1024
\
| nmrPipe -fn FT
\
| nmrPipe -fn PS -p0 90 -p1 0.0 -di
\
| nmrPipe -fn POLY -ord 0 -auto
\
| nmrPipe -fn TP
\
| nmrPipe -fn POLY -ord 0 -auto
\
-verb -ov -out test.ft3
pipe2ucsf test.ft3 HSQC.ucsf
\
2D Processing Done
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Simplified 2D
Reconstruction
ft12.com
nmrPipe -in data.fid \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.5 -end 0.98 -size 512 -c 1.0 \
| nmrPipe -fn ZF -size 1024 \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 -120.0 -p1 0.0 -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 0.98 -c 0.5 -size 512 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 -90.0 -p1 0.0 -di -verb \
| nmrPipe -fn POLY -ord 0 -auto \
| nmrPipe -fn TP \
| nmrPipe -fn POLY -ord 0 -auto \
-ov -out test.ft12
Looks great!
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.
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3D Spectra Conversion
fid.com
#!/bin/csh
bruk2pipe -in ./ser \
-bad 0.0 -noaswap -DMX -decim 24 -dspfvs 12 -grpdly 0
-xN
2048 -yN
4 -zN
-xT
1024 -yT
2 -zT
-xMODE
DQD -yMODE
Real -zMODE
-xSW
7002.801 -ySW
1824.818 -zSW
-xOBS
500.132 -yOBS
50.684 -zOBS
-xCAR
4.772 -yCAR
119.571 -zCAR
-xLAB
HN -yLAB
15N -zLAB
-ndim
3 -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?
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818
409
Real
2777.778
125.780
176.054
13C
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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
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2 FIDs for each indirect dimension.
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This is how the Pulse Program Acquires the data
•E.g. 2 FIDs for Nitrogen (a complex point)
• 2 FIDs for Carbon (a complex point)
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Then there are 818 points acquired. -zN = 818
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We treat each FID is real for conversion
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| nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr \
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Here the Y dimension (Nitrogen) is labeled as Rance-Kay (Echo-AntiEcho).
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.
Direct Dimension Transform
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ft1xyz.com
xyz2pipe -in fid/test%03d.fid -x \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.3 -end 0.98 -pow 2 -c 1.0 -size 512 \
| nmrPipe -fn ZF -size 512
\
| nmrPipe -fn FT -verb
\
| nmrPipe -fn PS -p0 -34.4 -p1 0.0 -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.
Direct Dimension Processing Only
Phase, Transpose for
Reconstruction
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ft1.com
xyz2pipe -in fid/test%03d.fid -x \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.3 -end 0.98 -pow 2 -c 1.0 -size 512 \
| nmrPipe -fn ZF -size 512
\
| nmrPipe -fn FT -verb
\
| nmrPipe -fn PS -p0 -34.4 -p1 0.0 -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.
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Fill in with Blanks,
Reconstruct
ist.csh
#!/bin/csh -xv
set F = $1
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}
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-xN
and -yN canfrom
be replaced
with -autoN
which gets the limits of
reconstruction
the schedule
file
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Each file in ‘yzx’ directory needs to be processed this way.
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Opportunity for parallelization of this process.
Cluster Submission
• E.g.
• foreach F (yzx/test*.ft1)
• qsub -cwd ./ist.csh $F
• end
• Many other methods. Consult your
sys/cluster admin.
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
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Running at 100% will make things toasty. You can
run at 50% etc etc.
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This will take 15-30 minutes for typical spectra....
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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
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FIDs
step are fully reconstructed from last
FIDs are now in conventional order
(planes)
xproj and yproj give the first plane in
each indirect dimension - for phasing.
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Lets look at yz.ft1
Projection Phasing
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Final Processing
ft23.com
#!/bin/csh -f
xyz2pipe -in rec/test%03d.ft1 -x \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
| nmrPipe -fn ZF -size 64
\
| nmrPipe -fn FT -verb
\
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di
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| nmrPipe -fn REV -verb \
| nmrPipe -fn TP \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
| nmrPipe -fn ZF -size 128
\
| nmrPipe -fn FT -alt -verb
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\ nmrPipe -fn PS -p0 0.0 -p1 0.0 -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
Nice Spectrum!