[Question from NMRWiki Q&A forum] simulate 3D NOESY

[nmrlearner]

simulate 3D NOESY

Hello everyone

I am using NMRPipe to simulate 3D, noise-free NOESY spectra (13C or 15Nresolved) from peak lists, but I have encountered some problems.

1) Peaks may spread over the entire z-dimension, even though I set a lowlinebroadening value.

2) Peaks are not fully symmetrical, and they have a "ragged" appearancealong the heavy atom-dimension.

I would greatly appreciate your help, either with NMRPipe or through pointing me to another good tool I can use for spectra simulation. Thank you very much in advance.

This is the script I run to simulate the FID:

#!/bin/cshsimTimeND -in c13.tab \ -xN 1024 -yN 256 -zN 420 \ -xT 512 -yT 128 -zT 210 \ -xMODE Complex -yMODE Complex -zMODE Complex \ -xSW 11203.13 -ySW 13079.5 -zSW 4577.64 \ -xOBS 800.000000 -yOBS 201.000000 -zOBS 800.000000 \ -xCAR 4.719000 -yCAR 42.146 -zCAR 2.2400000 \ -xLAB H -yLAB C -zLAB H \ -ndim 3 \ -aq2D States \ -out c13-fid/test%03d.fid -verb -ovAnd this I use to process the time-domain signal to get the spectrum:

#!/bin/cshxyz2pipe -in c13-fid/test%03d.fid -x -verb \| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \| nmrPipe -fn EM -lb 15 \| nmrPipe -fn GM -g1 0 -g2 0 -g3 0 \| nmrPipe -fn ZF -size 1024 \| nmrPipe -fn FT \| nmrPipe -fn PS -p0 0 -p1 0.0 -di \| nmrPipe -fn TP \| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \| nmrPipe -fn EM -lb 8 \| nmrPipe -fn GM -g1 0 -g2 0 -g3 0 \| nmrPipe -fn ZF -size 256 \| nmrPipe -fn FT \| nmrPipe -fn PS -p0 0 -p1 0 -di \| pipe2xyz -out c13-ft/test%03d.ft2xyz2pipe -in c13-ft/test%03d.ft2 -z -verb \| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \| nmrPipe -fn EM -lb 12 \| nmrPipe -fn GM -g1 0 -g2 0 -g3 0 \| nmrPipe -fn ZF -size 420 \| nmrPipe -fn FT \| nmrPipe -fn PS -p0 0 -p1 0 -di \| pipe2xyz -out c13-ft/test%03d.ft3xyz2pipe -in c13-ft/test%03d.ft3 -verb > c13.pipe/usr/local/soft/sparky-3.106/bin/pipe2ucsf c13.pipe c13.ucsfHere is a (much shortened) sample peak file:

VARS INDEX X_AXIS Y_AXIS Z_AXIS XW YW ZW HEIGHTFORMAT %5d %8.3f %8.3f %8.3f %7.3f %7.3f %7.3f %+eNULLVALUE -666NULLSTRING * 1 258.931 180.105 68.350 0.000 0.000 0.000 +3.391000e+00

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