Hi Peixiang. I started the R1rho tutorial at the wiki, which I think you refer to: http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_r1rho_fixed_time_recorded_on_varian_as_sequential_spectra
But I did not have the time to finish it. But, if you are a little adventurous, you can find the rest of the script that will finish it. We use something in relax called "system tests". This is to make sure, that everything keeps on functioning as we change code. Actually, that tutorial on the wiki is a translation of one of those systemtests. Try look in the relax software folder. test_suite/shared_data/dispersion/Kjaergaard_et_al_2013 Have a look at r1rho_1_ini.py r1rho_3_spectra_settings.py r1rho_4_run.py Try have a look on these. Do not look at the rx_XX.py file. That is scrap. But please double check everything. I is a little while ago :-) Double check with the systemtest here: test_suite/system_tests/relax_disp.py Look for: def test_r1rho_kjaergaard(self): all "self.interpreter." should be deleted for the script. .-) And remember to read in R1 data: relax_data.read(ri_id='R1', ri_type='R1', frq=cdp. See http://wiki.nmr-relax.com/DPL94#Essentials ---- If you find this helpful, you could maybe continue this R1rho tutorial at the wiki? I wrote the tutorial, because I know the learning curve is steep. And it have helped our students in the lab since. Best Troels 2014-05-22 17:13 GMT+02:00 Troels Emtekær Linnet <tlin...@nmr-relax.com>: > Hi Peixiang. > > For model selection, try this in relax. > The help section is the best you can get ! > > Just start relax in terminal: >> relax > > Then write: > relax> help(relax_disp) > to see all options. > > For example: > help(relax_disp.select_model) > You can find more info at the wiki: > http://wiki.nmr-relax.com/Category:Relaxation_dispersion > > Here you can find link to the online HTML manual, and the API documentation. > > You may want to read: > help(relax_disp.exp_type) > help(spectrum) > help(spectrum.replicated) > help(spectrum.baseplane_rmsd) > help(spectrometer) > > This a very very fast an useful method to quickly understand the functions. > > If you are unsure how to find where each method function is put, start the > GUI. > In the top menu, go through the settings. > They are ordered the same way. ! :-) > > For example. > help(grid_search) > > 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
