Hi Atul, As Troels asked, could you create a support request with the link https://gna.org/support/?func=additem&group=relax and attach the files there? Files should not be attached to public mailing list messages as it puts a large amount of strain on the infrastructure, not only with the mail server but also the 4 independent mailing list archives:
https://mail.gna.org/public/relax-users/2014-08/msg00025.html http://www.mail-archive.com/relax-users@gna.org/msg01672.html http://thread.gmane.org/gmane.science.nmr.relax.user/1735/focus=1736 http://marc.info/?l=relax-users&r=1&w=2 As you can see from these archived messages, your attachment has been stripped out of your email. The relax mail server is configured to delete all attachments before sending out the message. For your problem, I think I might now understand the issue. But it would still be useful to have the files attached to the support request for future reference. If you would like to keep the data private, then maybe delete all data in the files except for one or two residues (this also helps for converting the data into a relax system test). And you could also slightly randomise the peak intensity values if you really want to keep the real data private. The issue is that the ordering of relaxation dispersion data in relax is as follows: 1) Experiment type (certain dispersion models handle mixed experiment types, for example the MMQ models, 2) The spins of the cluster, 3) Magnetic field strength, 4) Offsets (for both R1rho and CPMG, though off-resonance CPMG models such as in CATIA are yet to be added to relax), 5) Dispersion points (nu_CPMG and nu_1). So for 5), you only have one point per offset. But to specify the reference, this needs to be at the lower dispersion point level. So for each offset value, you will need to have your reference and the point. You need to make relax load the reference peak intensities multiple times, once for each offset value. So maybe you need: --------------------------------------------------------------------------------------------------------------------------------------------------------------------- data = [ ['900MHz_reference', 'ref_off_reso_R1rho_ubi_1.list', 2100, None, 0.320, 900.0e6, 90000], ['900MHz_2100', '2100_off_reso_R1rho_ubi_2.list', 2100, 1500, 0.320, 900.0e6, 90000], ['900MHz_reference', 'ref_off_reso_R1rho_ubi_1.list', 2728, None, 0.320, 900.0e6, 90000], ['900MHz_2728', '2728_off_reso_R1rho_ubi_3.list', 2728, 1500, 0.320, 900.0e6, 90000], ['900MHz_reference', 'ref_off_reso_R1rho_ubi_1.list', 3357, None, 0.320, 900.0e6, 90000], ['900MHz_3357', '3357_reso_R1rho_ubi_4.list', 3357, 1500, 0.320, 900.0e6, 90000], ['900MHz_reference', 'ref_off_reso_R1rho_ubi_1.list', 3985, None, 0.320, 900.0e6, 90000], ['900MHz_3985', '3985_off_reso_R1rho_ubi_5.list', 3985, 1500, 0.320, 900.0e6, 90000], ['900MHz_reference', 'ref_off_reso_R1rho_ubi_1.list', 4614, None, 0.320, 900.0e6, 90000], ['900MHz_4614', '4614_off_reso_R1rho_ubi_6.list', 4614, 1500, 0.320, 900.0e6, 90000], ['900MHz_rep_4614','4614_rep_off_reso_R1rho_ubi_10.list', 4614, 1500, 0.320, 900.0e6, 90000], ['900MHz_reference', 'ref_off_reso_R1rho_ubi_1.list', 5242, None, 0.320, 900.0e6, 90000], ['900MHz_5242', '5242_off_reso_R1rho_ubi_7.list', 5242, 1500, 0.320, 900.0e6, 90000], ['900MHz_reference', 'ref_off_reso_R1rho_ubi_1.list', 5871, None, 0.320, 900.0e6, 90000], ['900MHz_5871', '5871_off_reso_R1rho_ubi_8.list', 5871, 1500, 0.320, 900.0e6, 90000], ['900MHz_reference', 'ref_off_reso_R1rho_ubi_1.list', 6500, None, 0.320, 900.0e6, 90000], ['900MHz_6500', '6500_off_reso_R1rho_ubi_9.list', 6500, 1500, 0.320, 900.0e6, 90000] ] --------------------------------------------------------------------------------------------------------------------------------------------------- Please carefully check the printouts to make sure the correct numbers are being sent into the correct user functions. Specifying the reference at the higher offset level is not yet supported in relax. But with your data set attached to a support request, maybe in the future it could be turned into a relax system test and such a feature implemented. I hope this information helps. Regards, Edward On 22 August 2014 23:01, Atul Srivastava <asriv...@umn.edu> wrote: > Dear Edward, > > Thanks for providing help and insights. I used an improved script. The > scripts is able to calculate the R2eff and the omegaeffective properly, but > it is not able to fit any model. It also sees dispersion point as a constant > 1500 Hz (see attached file in results/R2eff/disp_55_N.out). > > I have attached all sample data, script and results for your review. Please > see the last few lines in the log file for the error message. > > Thanks, > Atul > > > > > On Fri, Aug 22, 2014 at 3:02 AM, Edward d'Auvergne <edw...@nmr-relax.com> > wrote: >> >> Hi Atul, >> >> Again continuing from Troels' post at >> http://thread.gmane.org/gmane.science.nmr.relax.user/1718/focus=1732. >> Well, actually, as Troels fully covered all of you questions in more >> detail than I could have provided, I don't have anything to add. If >> you have other questions, please don't hesitate to ask. >> >> Regards, >> >> Edward >> >> >> On 21 August 2014 12:00, Troels Emtekær Linnet <tlin...@nmr-relax.com> >> wrote: >> >> [snip] >> >> > relax_disp.relax_time(spectrum_id=id, time=relax_time) >> > -> This is used for the initial R2eff calculation, for exponential >> > curve fitting. >> > >> > # Set the NMR field strength of the spectrum. >> > spectrometer.frequency(id=id, frq=H_frq) >> > -> This is used for conversion between nucleus, etc. >> > >> > # Load the R1 data. >> > relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6, >> > file='R1_500MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2, >> > res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, >> > error_col=7) >> > -> R1 needs to be loaded. This is because that R1 is part of the >> > equations. :-) The next release of relax, will implement feature where >> > R1 is fitted. >> >> Note, that fitting introduces another variable in the equations. >> > >> > # Read the chemical shift data. >> > chemical_shift.read(file='ref_500MHz.list', dir=DATA_PATH) >> > >> > -> This is needed to get the ppm position of the nucleus. >> > -> See now: >> > http://www.nmr-relax.com/manual/Dispersion_model_summary.html >> > -> The "average resonance in the rotating frame" Omega(bar) = w_(bar) - >> > w_rf." >> > -> Here w_bar is the chemical shift, and w_rf is the offset. >> > -> Let is review figure Fig1_Palmer_Massi_2006.png >> > -> This is the S_z axis. >> > >> > That should be it. >> > >> > If you have any questions, please don't hesitate to write again. >> > >> > If you need more help, consider writing a support request on the >> > homepage tracker. >> > - https://gna.org/support/?group=relax >> > >> > Add following information: >> > # Please attach a system info file >> >> relax -i -t relax_i.txt >> > >> > # Please write up, which buttons you pushed, or attach your script. >> > # Consider adding your data in "sample" format. Meaning that you >> > delete all confidential information from the files, and only have 1-2 >> > residues left for testing. >> > >> > If you write such a support request, it it easier to share script files, >> > and >> > help other users. >> > >> > The benefits from such a support request is: >> > - The information is available to all users, which can benefit >> > others in same situation. >> > - The information can be tracked back. >> > - The relax manual can be expanded, to help future users in same >> > situation. >> > >> > >> > Good luck! >> > >> > Best >> > Troels Emtekær Linnet >> > PhD student >> > Copenhagen University >> > SBiNLab, 3-0-41 >> > Ole Maaloes Vej 5 >> > 2200 Copenhagen N >> > Tlf: +45 353-22083 >> > Lync Tlf: +45 353-30195 > > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
