[firstnumber=11] # Load the reference spectrum and saturated spectrum peak intensities. spectrum.read_intensities(file='ref.list', spectrum_id='ref_ave') spectrum.read_intensities(file='sat.list', spectrum_id='sat_ave')
will load the peak heights of the reference and saturated NOE experiments (although the volume could be used instead). relax will automatically determine the format of the peak list. Currently only Sparky, XEasy, NMRView and a generic columnar formatted text file are supported.
In this example, relax will determine from the file contents that these are Sparky peak lists (saved after typing “lt”). The first column of the file should be the Sparky assignment string and it is assumed that the 4 th column contains either the peak height or peak volume (though this can be in any column - the int_col argument is used to specify where the data is). Without specifying the int_method argument, peak heights will be assumed. See page for a description of all the spectrum.read_intensities user function arguments. In this example, the peak list looks like:
Assignment w1 w2 Data Height LEU3N-HN 122.454 8.397 129722 GLY4N-HN 111.999 8.719 422375 SER5N-HN 115.085 8.176 384180 MET6N-HN 120.934 8.812 272100 ASP7N-HN 122.394 8.750 174970 SER8N-HN 113.916 7.836 218762 GLU11N-HN 122.194 8.604 30412 GLY12N-HN 110.525 9.028 90144
For subsequent usage of the data in relax, assuming a 3D structure exists, it is currently advisable to use the same residue and atom numbering as found in the PDB file.
If you have any other format you would like read by relax please send an email to the relax development mailing list detailing the software used, the format of the file (specifically where the residue number and peak intensity are located), and possibly attaching an example of the file itself.
The relax user manual (PDF), created 2019-06-14.