NUS 3D NMR spectra process notes

nmrPipe scripts for processing NUS 3D NMR spectra:

  1. Copy the two and into your 3D fid directory.
  2. After extract the water peak reference and necessary processing parameters, update those parameters in, (for example, for the third dimension, both -zN and –zT should be equal to niXni2.) also update the ghn_ca_cb_S.hdr_3 file name. Start to process it and get the right zero-order phase correction and re-process it.
  3. Update the zero-order phase correction in first part of the file, and the output nv filename in the bottom part, and start to process it. It take some time (~10 minutes), depends on the HN dimension spectrum rang you choose.
  4. Use nmrDraw to check three output *.dat files from macro proj3D.tcl, and if the phases of N15 and C13 dimensions look not right, just use to re-correct the phases without doing the re-construction part.
  5. The next two scripts are working OK for the phase array=”phase,phase2″; if phase array=”phase2,phase”, first you DON’T need to reverse the schedule file; second you need to reverse the (2nd) N15 and (3rd) C13 columns in the first part of script; third you need to use  ranceZphf.M instead of ranceY.M if it’s Rance-Kay exp., if it’s hcch-cosy or hcch-tocsy exp., both macros should be commented out.
## Adjust the name of your schedule at the top
## Adjust sweep widths, carrier frequencies, and spectrometer frequencies
## In the var2pipe section.
## -yMODE and -zMODE must BOTH be Real
## -yN must be 4
## -zN must be the length of your schedule
## If you need Rance-Kay for the Nitrogen dimension, use the ranceY macro
## at the bottom of the section.
## After running this script once and adjusting your phase correction,
## enter that phase correction in the bottom section.
rr ghc_co_nh_S.hdr_3 > ./reversed.sched
rm -rf data
var2pipe -in ./fid \
-noaswap -aqORD 1 \
-xN 2048 -yN 4 -zN 1600 \
-xT 1024 -yT 4 -zT 1600 \
-xMODE Complex -yMODE Real -zMODE Real \
-xSW 11261.261 -ySW 2268.9886 -zSW 11261.2613 \
-xOBS 799.7105 -yOBS 81.034 -zOBS 799.7105 \
-xCAR 4.6080 -yCAR 116.5048 -zCAR 4.6080 \
-xLAB HN -yLAB N15 -zLAB H1 \
-ndim 3 -aq2D States \
| nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr \
#| nmrPipe -fn MAC -macro ~/bin/IST/ranceZphf.M -noRd -noWr \
| pipe2xyz -x -out ./data/test%03d.fid -verb -ov
rm -rf xyz
xyz2pipe -in data/test%03d.fid -x \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 1.0 -size 512 \
| nmrPipe -fn ZF -size 2048 \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p0 -49.0 -p1 0.0 -di \
| nmrPipe -fn EXT -left -sw \
#| nmrPipe -fn EXT -x1 6.4ppm -xn 10.2ppm -sw \
| pipe2xyz -ov -out xyz/test%03d.nus -x
nmrDraw xyz/test001.nus
#!/bin/csh -f
## Enter your phase correction in the top xyz2pipe section.
## Make sure the EXT step gives adequate width for your spectrum. The
## reconstruction goes faster if you remove the empty edges of your spectrum,
## but don’t cut too much!
## Adjust the name of your output at the bottom.
## You may need to make another copy of the bottom section in order
## To make adjustments to the final processing step without repeating
## the reconstruction. (
rm -rf yzx # clean up
rm -rf yzx_ist # clean up
rm -rf rec
rm -f *.dat
mkdir yzx
mkdir yzx_ist
mkdir rec
xyz2pipe -in data/test%03d.fid -x \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 1.0 -size 512 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p0 -49.0 -p1 0.0 -di \
| nmrPipe -fn EXT -x1 6.3ppm -xn 9.5ppm -sw \
| pipe2xyz -ov -out yzx/test%03d.nus -z
/home/wuhw/Downloads/NUS_macro_wagner_lab/HNCO_example/parallel -j 100% ‘/home/wuhw/ist.csh {} > /dev/null; echo {}’ ::: yzx/test*.nus
xyz2pipe -in yzx_ist/test%03d.phf | /home/wuhw/Downloads/Linux_i686/phf2pipe_20130510_64b -user 1 -xproj xz.ft1 -yproj yz.ft1 | pipe2xyz -out rec/test%03d.ft1
xyz2pipe -in rec/test%03d.ft1 -x \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p0 0 -p1 0.0 -di \
| nmrPipe -fn TP \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT -neg -verb \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \
| nmrPipe -fn TP \
| nmrPipe -fn ZTP \
> rec/data.pipe
pipe2xyz -in rec/data.pipe -out rec/test%03d.ft3 -x
xyz2pipe -in rec/test%03d.ft3 -verb \
| pipe2xyz -out hcconh.nv -nv -ov
proj3D.tcl -in rec/test%03d.ft3
#xyz2pipe -in rec/test%03d.ft3 -x -out HNCACB.pipe
#pipe2ucsf HNCO.pipe HNCO.ucsf
* the above two scripts are mainly from Katie’s notes, and just for local users.

started on Jan. 16, 2014

updated on Junn 30, 2015

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