NOE script mode - loading the data

The commands

# 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 2020-08-26.