Dear Christina. I think Edward is on vacation, but maybe I can help.
I have only worked on the dispersion part of relax and by no means expert on the model free part. But I understand the data structure of relax and can maybe help with a script for your analysis. Can you provide a description of where you are in the process, and what you aim for.? Best Troels Den 13. nov. 2015 12.12 PM skrev "Christina Möller" <c.moel...@fz-juelich.de >: > Dear Edward, > > thank you so much for your recommendations and the really helpful wiki > article about the CGS and SI unit system. Now I understand the equation > differences and successfully back-calculated my relaxation data. > > Furthermore, I used the generate_ri.py script and the back-calculated > values are close to the experimental data (as expected). I have to admit > that I copied the motion parameters (s2,sf2,s2s,tf, etc) and the > associated model manually into the script and executed the script > several times for different residues. I am pretty sure that it is > possible to include one or several lists in order to automatically > update these parameters for each residue and run this script only one > time. Unfortunately, I was not able not find out how this works. Could > you give me an idea? > > Thanks, > Christina > > > > Am 11/05/2015 um 03:53 PM schrieb Edward d'Auvergne: > >> Hi Christina, >> >> Please see below: >> >> On 5 November 2015 at 14:05, Christina Möller <c.moel...@fz-juelich.de> >> wrote: >> >>> Dear Edward and relax-users, >>> >>> I am sorry to ask you again for some advice to back calculate the >>> relaxation >>> data from the model parameter values. Here is what I tried so far: >>> For the back calculation I loaded the final results determined by the >>> automated analysis using the dauvergne_protocol.py into the relax gui. >>> Then >>> I selected the back_calc tool from user functions -> relax_data. >>> After starting the back calculation without any entry >>> relax> relax_data.back_calc(ri_id=None, ri_type=None, frq=None) >>> I get the following error message: >>> RelaxWarning: comparison to `None` will result in an elementwise object >>> comparison in the future. >>> >> This is a warning produced by more recent versions of the numpy Python >> package. It is harmless message about changes which will occur in >> numpy, and it is safe to ignore. Note that I have fixed this in the >> source code repository and the fix will appear in the future when I >> release relax 4.0.1 (it is not present in relax 4.0.0 at >> http://wiki.nmr-relax.com/Relax_4.0.0 ). This was first reported at: >> >> [relax-users] RelaxWarning: comparison to `None` will result in an >> elementwise object comparison in the future ( >> http://thread.gmane.org/gmane.science.nmr.relax.user/1839 ). >> >> And the solution at: >> >> [relax-users] Re: RelaxWarning: comparison to `None` will result >> in an elementwise object comparison in the future ( >> http://thread.gmane.org/gmane.science.nmr.relax.user/1844 ). >> >> >> If I put the frequency in >>> relax> relax_data.back_calc(ri_id=None, ri_type=None, frq=599468076.0) >>> I get another error message >>> Traceback (most recent call last): >>> File >>> >>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/gui/interpreter.py", >>> line 306, in run >>> fn(*args, **kwds) >>> File >>> >>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/pipe_control/relax_data.py", >>> line 132, in back_calc >>> spin.ri_data_bc[ri_id] = api.back_calc_ri(spin_index=spin_index, >>> ri_id=ri_id, ri_type=ri_types[ri_id], frq=frqs[ri_id]) >>> KeyError: 'R1_600' >>> >>> Can you give me a hint what I am doing wrong? >>> >> I would suggest using the sample_scripts/model_free/generate_ri.py >> sample script. The relax_data.back_calc user function requires that >> the relaxation data ID, the relaxation type, and frequency arguments >> be supplied to correctly calculate the desired data (see >> http://www.nmr-relax.com/manual/relax_data_back_calc.html ). Without >> this information, relax cannot determine what you would like to do. >> Using the sample script would be the easiest option. >> >> >> I know that the relaxation data can also be back calculated using the >>> equations 7.3a - 7.8 in the relax manual (PDF), although it is not that >>> trivial for an ellipsoid model because I need to determine the weights. >>> Is >>> there a reason why you define c=1/3(ωH*∆σ)^2 (eq. 7.5) instead of >>> c=2/15(ωN*∆σ)^2 like it can be found in literature? >>> >> These two factors come from using CGS vs. SI units. I have mentioned >> this issue before (see >> http://thread.gmane.org/gmane.science.nmr.relax.devel/1023/focus=1034 >> ). I have also started a stub wiki article to help explain these >> differences - http://wiki.nmr-relax.com/CGS_versus_SI . In SI units >> the correct unit (squared) is (ω·∆σ)^2 / 3, and SI units are used >> throughout relax. This has made some parts of relax more difficult to >> implement as there are many equations in the literature in CGS units, >> and the authors will often not identify this older system. Some >> stubborn people just prefer the magnetic constant to be 1 rather than >> µ0/(4π), and will not shift from the CGS metric system to the SI >> metric system. >> >> Regards, >> >> Edward >> >> > > -- > ------------------------------------------------------------ > Christina Möller > ICS-6 / Structural Biochemistry > Forschungszentrum Jülich > D-52425 Jülich > GERMANY > > E-mail: c.moel...@fz-juelich.de > Tel.: +49-2461-619387 > Fax +49-2461-619387 > > > > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > > > _______________________________________________ > 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 > _______________________________________________ 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
