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)


Is it possible in NMRPipe to:

  1. Generate a peak table for a new spectrum using the resonance positions in an existing peak table?
  2. Update the peak intensities in the existing peak table from the current spectrum?

I have a set of relaxation data, and currently to obtain peak heights at different delays I have to manually define the peaks in all HSQCs, which is rather time consuming. Furthermore, if I decide to re-process the spectra, the previously generated peak tables are useless, as the peak heights are read from the peak table file, rather than from the current spectrum.

Ideally, what I am looking for is:

  1. Generate an assigned peak table for the first spectrum.
  2. Load i-th spectrum, use the assigned peak table to define the resonances in the i-th spectrum.
  3. Read the intensities at given resonance positions in the i-th spectrum and write them to the new peak table.

Thank you,


asked Aug 21 '11 at 14:32

vvostri's gravatar image


Question solved: autoFit.tcl can generate a new peak table for a new spectrum, using the resonances from an existing peak table. - vvostri (Aug 23 '11 at 13:58)

One Answer:
i like this answer (click again to cancel)
i dont like this answer (click again to cancel)

The command "lt" (small "L" and small "T") type on the sparky screen opens the peak list. There is an options tab once this is opened. Click on the options tab to allow for peak intensity readout. Click OK. Click update. Your peak list should have the associated peak intensity. Click save. The file generated upon saving is a ".list" file.
Open you new spectra and type "rp". This will allow you to read your saved peak list above on to the new spectra. Click browse to select your saved ".list" file. There is a drop down menu below your selected list file. Choose the spectra you want you peak list to be loaded in. You could load two peak lists on the same spectra so be careful. To redefine your peaks on this new spectra list, you can select the peaks individually by pressing "F1" and selecting you peak. Once the chosen peak is selected the ornament should be highlighted. You then can press "pc" to peak center. Go to you peak list by pressing "lt" again. Click update and save you peak list. You can select all peaks with the "pa" command. All of the above commands can be found in the menu by right clicking on the spectra or on the pointer mode ("F1") that is opened when you open a spectra. We have found that peak intensity is most consistent when you use the "rh" command, which takes a little setup and is used for relaxation measurements. You have to have all you spectra loaded, type "rh", setup "rh", click OK, type "pa", then type "rh" again. The rh file can be saved and peak intensity is one of the outputs of the file. The Sparky manual can be found online and is very complete. If I have a problem, I usually type the problem into Google with a Sparky following the problem, like (peak list Sparky).


answered Aug 23 '11 at 04:50

bmoret42's gravatar image


Thank you, bmoret42. I am familiar with Sparky, but would prefer NMRPipe-based solution. I was pointed toward autofit.tcl script which suits my needs. - vvostri (Aug 23 '11 at 13:56)

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