To load the peak intensities into relax the spectrum.read_intensities and relax_fit.relax_times user functions are executed. Important keyword arguments for these user functions are the file name and directory, the spectrum identification string and the relaxation time period of the experiment in seconds. By default the file format will be automatically detected. Currently Sparky, XEasy, NMRView, and generic columnar formatted peak lists are supported. To be able to import any other type of format please send an email to the relax development mailing list with the details of the format. Adding support for new formats is trivial. The following series of commands - an expansion of the for loop in the sample script - will load peak intensities from six different relaxation periods, four of which have been duplicated, from Sparky peak lists with the peak heights in the 10 th column.
[numbers=none] spectrum.read_intensities('T2_ncyc1.list', spectrum_id='1', int_col=10) relax_fit.relax_time(spectrum_id='1', time=0.0176) spectrum.read_intensities('T2_ncyc1b.list', spectrum_id='1b', int_col=10) relax_fit.relax_time(spectrum_id='1b', time=0.0176) spectrum.read_intensities('T2_ncyc2.list', spectrum_id='2', int_col=10) relax_fit.relax_time(spectrum_id='2', time=0.0352) spectrum.read_intensities('T2_ncyc4.list', spectrum_id='4', int_col=10) relax_fit.relax_time(spectrum_id='4', time=0.0704) spectrum.read_intensities('T2_ncyc4b.list', spectrum_id='4b', int_col=10) relax_fit.relax_time(spectrum_id='4b', time=0.0704) spectrum.read_intensities('T2_ncyc6.list', spectrum_id='6', int_col=10) relax_fit.relax_time(spectrum_id='6', time=0.1056) spectrum.read_intensities('T2_ncyc9.list', spectrum_id='9', int_col=10) relax_fit.relax_time(spectrum_id='9', time=0.1584) spectrum.read_intensities('T2_ncyc9b.list', spectrum_id='9b', int_col=10) relax_fit.relax_time(spectrum_id='9b', time=0.1584) spectrum.read_intensities('T2_ncyc11.list', spectrum_id='11', int_col=10) relax_fit.relax_time(spectrum_id='11', time=0.1936) spectrum.read_intensities('T2_ncyc11b.list', spectrum_id='11b', int_col=10) relax_fit.relax_time(spectrum_id='11b', time=0.1936)
The replicated spectra a set up with the commands
[firstnumber=47] # Specify the duplicated spectra. spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave']) spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave']) spectrum.replicated(spectrum_ids=['T2_ncyc9_ave', 'T2_ncyc9b_ave']) spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
Note that the relaxation time period should be calculated directly from the pulse sequence (as the sum of delays and pulses for the period), as the estimated time may not match the real time. For the Sparky peak lists, by default relax assumes that the intensity value is in the 4 th column. A typical file 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
By supplying the int_col argument to the spectrum.read_intensities user function, this can be changed. A typical XEasy file will look like:
No. Color w1 w2 ass. in w1 ass. in w2 Volume Vol. Err. Method Comment 2 2 10.014 134.221 HN 21 LEU N 21 LEU 7.919e+03 0.00e+00 m 3 2 10.481 132.592 HE1 79 TRP NE1 79 TRP 1.532e+04 0.00e+00 m 17 2 9.882 129.041 HN 110 PHE N 110 PHE 9.962e+03 0.00e+00 m 18 2 8.757 128.278 HN 52 ASP N 52 ASP 2.041e+04 0.00e+00 m 19 2 10.086 128.297 HN 69 SER N 69 SER 9.305e+03 0.00e+00 m 20 3 9.111 127.707 HN 15 ARG N 15 ARG 9.714e+03 0.00e+00 m
where the peak height is in the Volume column. And for an NMRView file:
label dataset sw sf H1 N15 cNTnC_noe0.nv 2505.63354492 1369.33557129 499.875 50.658000946 H1.L H1.P H1.W H1.B H1.E H1.J H1.U N15.L N15.P N15.W N15.B N15.E N15.J N15.U vol int stat comment flag0 0 {70.HN} 10.75274 0.02954 0.05379 ++ 0.0 {} {70.N} 116.37241 0.23155 0.35387 ++ 0.0 {} -6.88333129883 -0.1694 0 {} 0 1 {72.HN} 9.67752 0.03308 0.05448 ++ 0.0 {} {72.N} 126.41302 0.27417 0.37217 ++ 0.0 {} -5.49038267136 -0.1142 0 {} 0 2 {} 8.4532 0.02331 0.05439 ++ 0.0 {} {} 122.20137 0.38205 0.33221 ++ 0.0 {} -2.58034267191 -0.1320 0 {} 0
The relax user manual (PDF), created 2024-06-08.