i like this post (click again to cancel)
i dont like this post (click again to cancel) remove favorite mark from this question (click again to restore mark)

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:


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:


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 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.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:

FORMAT %5d %8.3f %8.3f %8.3f %7.3f %7.3f %7.3f %+e

    1  258.931  180.105   68.350   0.000   0.000   0.000 +3.391000e+00

asked Mar 14 '14 at 00:59

canavanin's gravatar image


updated Mar 14 '14 at 01:05

One Answer:
i like this answer (click again to cancel)
i dont like this answer (click again to cancel) the author of the question has selected this answer as correct


I wrote up a guide for myself to do this that works, although I've only done 2D simulated spectra, for example to look at an HSQC from protein assignments in the BMRB. I can post it if anyone wants it, keeping in mind that there are probably several ways to do this.

One thing that jumps out at me right away is that you aren't telling NMRPipe what linewidths the peaks should have - your XW, YW, and ZW values are all zero, so simTimeND is needing to guess. Note that the values need to be in points. Try setting reasonable values for those and see if your results improve.



answered Mar 18 '14 at 06:46

Andrew%20Fowler's gravatar image

Andrew Fowler

Andrew, thanks for your reply. I think I've found the problem and it actually had to do with the linewidths, as you suggested. I specify those in the 2nd script (the -lb parameter to the EM function), but they were too small for the number of points, so I got wiggles, hence the ragged-looking peaks. - canavanin (Mar 19 '14 at 05:17)

Your answer
Please start posting your answer anonymously - your answer will be saved within the current session and published after you log in or create a new account. Please try to give a good answer, for discussions, please use comments and please do remember to vote (login to vote)
toggle preview

powered by CNPROG