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hi,i want to run NOESYPHPR with increment time as zero (d0=0).If possible, which software is easy to stack plot(in 1D-format)them.

asked Nov 09 '10 at 02:18

saship21's gravatar image


updated Nov 09 '10 at 09:30

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev

d0 is the first value of the incremented delay in your 2D experiment, the actual increment value, as Clemens said is in0. That is it's the in0 controls how d0 is incremented. To do what you want you should either modify the pulse sequence or use some 1D NOESY experiment. - Evgeny Fadeev (Nov 11 '10 at 08:40)

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Do you want to just set d0=0 or do you want to have a zero incorement in0. The latter is not possible, because the spectral width is calculated from in0 and this would lead to a division by zero. Depending on the model spectrometer you have I would not recommend to set d0 to 0 either. To eliminate incrementation just comment out the command id0.

To create a stacked plot use the program split2D to split the 2D into individual 1D spectra, then use the plot editor of Topspin to create a stacked plot.


answered Nov 09 '10 at 03:15

Clemens%20Anklin's gravatar image

Clemens Anklin

actuvally i want to study how system varies with time..what i means is if i keep increments as zero so that i am imposing same conditions at every point of time.This my idea is it possible if not give me some suggesitons to solve this. thank you - saship21 (Nov 10 '10 at 21:37)

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Expanding on Clemens' answer... Line 38 in the file nmr/lists/pp/noesyphpr contains this:

d11 mc #0 to 2 F1PH(ip1 & ip29, id0)

The id0 bit instructs the pulse programmer to increment the d0 for each new experiment and ip1 & ip29 increments phases necessary to discriminate negative and positive frequencies in the indirect dimension. If you make that line look like: (that is replace with two lines below)

d11 wr #0 if #0 zd !write to file 0, increment file pointer (if) and zero new memory location
lo to 2 times td1 !go to label 2, repeat td1 times.

Then there will be no incrementation of the delay.

I thought at first that you could simply have:

d11 mc #0 to 2

but the pulse programming manual says that mc macro "can be used with one or more clauses, e.g. F1QF, which expands to a loop structure", so probably you want to specify the loop explicitly.

Since you need to edit a pulse sequence you should copy the file to some other name before editing it and type in the TOPSPIN or XWinNMR command line:

pulprog <the_new_pulseprogram_name>

You might also look into setting up an au (automation) program to run a kinetic experiment, if that's what your goal is.


answered Nov 11 '10 at 16:54

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev

updated Nov 11 '10 at 20:35

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