simulate 3D NOESY

Hello everyone

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

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

2) Peaks are not fully symmetrical, and they have a "ragged" appearance along 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/csh

simTimeND -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 -ov

And this I use to process the time-domain signal to get the spectrum:

#!/bin/csh

xyz2pipe -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 EXT -left -sw                      \
| 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                  \
#| nmrPipe  -fn TP                                 \
| pipe2xyz -out c13-ft/test%03d.ft2

xyz2pipe -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.ft3

xyz2pipe -in c13-ft/test%03d.ft3 -verb > c13.pipe
/usr/local/soft/sparky-3.106/bin/pipe2ucsf c13.pipe c13.ucsf

Here is a (much shortened) sample peak file:

VARS INDEX  X_AXIS Y_AXIS Z_AXIS XW YW ZW HEIGHT
FORMAT %5d %8.3f %8.3f %8.3f %7.3f %7.3f %7.3f %+e

NULLVALUE -666
NULLSTRING *
    1  258.931  180.105   68.350   0.000   0.000   0.000 +3.391000e+00

removed script lines that were commented out anyway

posted Mar 14 '14 at 01:05

canavanin
17