Re: field strength off-resonance R1rho constant relax time relaxation dispersion -- August 22, 2014 - 23:01

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 <edward@xxxxxxxxxxxxx>
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 <tlinnet@xxxxxxxxxxxxx>
> 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