Dear Peixiang. I have just discovered a bug in relax, where the 'relax_times' is not properly loaded from the data-store and sent to the target function of model NS R1rho 2-site.
This means that currently 'NS R1rho 2-site' can only be used for fixed time at the moment. This bug has no influence on all other R1rho models, as they don't use relax_time in their equations. Best Troels 2014-05-22 16:34 GMT+02:00 pma <peixiang...@ibs.fr>: > Hi, Edward, > > Thanks for you reply. I used the script mode in linux. > > I tried with 'r1rho_on_res_m61.py', but I think in the script it has a > mistake. > in line27 ds.fixed = True, I think it should be False, because this > experiment has different time period, they do not need the ref. I changed to > False, the M61 model still give right result. > > But I still have some other questions. > > 1. How did you declare replicates in such Variable relaxation period > experiments? I saw in the example r1rho_on_res_m61.py, you read all the data > into a big Matrix data and did not declare the replicate. But for the fixed > time period you declare by the spectrum ID. Did you have a solution for > this? > > 2. I want to test NS R1rho 2-site, so I simply add it into the MODELS in > 'r1rho_on_res_m61.py'. It seems does not work. > first, they give the warning when it comes to NS R1rho 2-site, (grid_inc =8 > ) > ------------------------------------------------------------------------------------------------------------------------------ > Searching through 32768 grid nodes. > lib/dispersion/ns_r1rho_2site.py:118: RuntimeWarning: divide by zero > encountered in double_scalars > theta = atan(spin_lock_fields[i]/dA) > lib/dispersion/ns_r1rho_2site.py:132: RuntimeWarning: invalid value > encountered in double_scalars > back_calc[i]= -inv_relax_time * log(MA) > ----------------------------------------------------------------------------------------------------------------------------- > I think the grid search is too heavy for the NS model, do you have a > solution to constrain it? > > Or for example, if I want to limit grid search only for kex and pA, but not > for others, how can I declare that? > > For RuntimeWarning: divide by zero encountered in double_scalars, do you > have suggestions for this? > > The final results for 'NS R1rho 2-site' did not fit at all, so the data for > M61 can only be fit with M61 model but not other models? > > Thanks a lot! > > Peixiang > > > On 05/19/2014 05:49 PM, Edward d'Auvergne wrote: >> >> Hi Peixiang, >> >> Welcome to the relax mailing lists! The relaxation dispersion >> analysis implemented in relax is quite flexible, and the data you have >> is supported. This is well documented in the relax manual which you >> should have with your copy of relax (the docs/relax.pdf file). Have a >> look at section 'The R2eff model' in the dispersion chapter of the >> manual (http://www.nmr-relax.com/manual/R2eff_model.html), >> specifically the 'Variable relaxation period experiments' subsection. >> >> Unfortunately the sample scripts are all for the fixed time dispersion >> experiments. However you could have a look at one of the scripts used >> for the test suite in relax: >> >> test_suite/system_tests/scripts/relax_disp/exp_fit.py >> >> This script is run in the test suite to ensue that the data you have >> will always be supported. There are many more scripts in that >> directory which you might find interesting. The 'r1rho_on_res_m61.py' >> script also involve an exponential fit with many different relaxation >> time periods. >> >> You could also try using the relax graphical user interface (GUI) by >> running: >> >> $ relax -g >> >> Here you simply load the peak list data via the 'Add' button in the >> 'Spectra list' GUI element and, when you reach the relaxation time >> wizard page, simply specify different times for the different spectra >> - relax will handle the rest. Have a look at >> http://www.nmr-relax.com/manual/Dispersion_GUI_mode_loading_data.html >> (the GUI section of the dispersion chapter). The GUI should be much >> easier to use than the script UI, though a lot less flexible if you >> wish to perform custom, non-standard analyses. >> >> Regards, >> >> Edward >> >> >> >> On 19 May 2014 16:25, pma <peixiang...@ibs.fr> wrote: >>> >>> Hi, all, >>> >>> Did anybody manage to fit the R1rho relaxation dispersion from some >>> calculated R2 data (e.g. I fitted the different relax_delay time to >>> extract >>> R1rho, then calculate R2 = R1rho/sin^2 - R1/tan^2 ) >>> >>> I found a tutorial on wiki, but it stopped after processing the spectra, >>> actually I finished this part already. Besides,in the manual for R1rho >>> calc >>> (page 173 in the manual) in the R2eff model, it defined >>> R1rho(w1)=-1/T*ln(I1(w1)/I0), e.g. it assume the mono-dispersion between >>> time 0 and a fix time point. We did a bit different, we recorded a series >>> of >>> time points and got the R1rho for each w1. >>> >>> Now I have all the R2s, I want to use the implemented R1rho models to fit >>> my >>> data. >>> >>> I think relax should be possible to do the fitting with custom calculated >>> R2, what kind of format should I use? Can anyone show an example of >>> import >>> file and the processing scripts? Then I could reformat my data to the >>> template format. >>> >>> Now my data looks like the following: for each RF_frq the R2 has such >>> format >>> >>> res_num w1(Hz) value error >>> 1 1200 30.7734534261 2.68087025208 >>> 1 2000 23.0503960923 1.53567705225 >>> ................... >>> >>> >>> Thanks a lot! >>> >>> Peixiang >>> >>> On 05/16/2014 02:18 PM, relax-users-requ...@gna.org wrote: >>>> >>>> Welcome to the relax-users@gna.org mailing list! >>>> >>>> To post to this list, send your message to: >>>> >>>> relax-users@gna.org >>>> >>> _______________________________________________ >>> 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 _______________________________________________ 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
