Hi Peixiang, Actually, for comparison purposes for applying the 'NS R1rho 2-site' model (http://wiki.nmr-relax.com/NS_R1rho_2-site) to variable-time R1rho-type data, Art Palmer's MP05 model would be much better (http://wiki.nmr-relax.com/MP05) than the DPL94 model (http://wiki.nmr-relax.com/DPL94) as it is of much higher quality. Andy Baldwin apparently has derived an even better analytic model, especially when R20A and R20B are significantly different, see:
http://gna.org/support/?3155#comment0 and the discussions in the thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5414/focus=5447 and: http://thread.gmane.org/gmane.science.nmr.relax.devel/5410/focus=5433 This last thread is about the B14 model (Baldwin 2014, http://wiki.nmr-relax.com/B14) implemented in relax by Troels Linnet, but there are mentions of Andy's R1rho model. However the R1rho model from Andy is not implemented in relax yet. Do you have much experience with variable-time R1rho numeric models? Looking at the code for where the relax_time variable comes from, it is not very clear which relaxation time is being used: http://www.nmr-relax.com/api/3.2/specific_analyses.relax_disp.data-module.html#loop_time >From the code itself: http://www.nmr-relax.com/api/3.2/specific_analyses.relax_disp.data-pysrc.html#loop_time it looks like this loop_time() function assumes fixed-time data and hence only the first encountered time value for the given experiment, magnetic field strength, offset, and dispersion point is used. So your expertise will be very useful for resolving this variable-time R1rho numeric model problem! Note that there are a few improvements to the R1rho models that are yet to be implemented in relax: http://thread.gmane.org/gmane.science.nmr.relax.devel/5414/focus=5808 http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html Cheers, Edward On 11 June 2014 10:07, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Hi Peixiang, > > Please see below: > > >> Congratulations about the new version of 3.2.2, I tried, it works well :) > > Cheers. If you notice any other problems or strange behaviour, please > don't hesitate to submit a bug report > (https://gna.org/bugs/?func=additem&group=relax). Then that problem > will likely be fixed for the next relax version. > > >> Still one question of using the different relaxation time periods. >> >> My R1rho RD experiment has different relaxation time periods, I could input >> all the peaks by the loop. >> >> Then I fit with 'NS 2-site R1 model', they could also do the fitting and >> give the results and also a nice fitting of the dispersion curve. >> Still I did not figure out, which Trelax is it using in the NS model in the >> case of different relaxation time periods. >> Only the last relaxation time period? Then fit as fixed time experiment? > > As this code was directly contributed by Paul Schanda and Dominique > Marion, and I'm guessing that their offices are not too far from yours > at the IBS, maybe you could ask them directly ;) Well, it was Paul > who organised that the code be contributed to relax. In reality the > original authors were Nikolai Skrynnikov and Martin Tollinger. The > API documentation is also a useful resource for answering such > questions (http://www.nmr-relax.com/api/3.2/). For this, see the > relax library documentation for that model: > > http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-module.html > > This documentation describes the origin and history of the code. You > could even look at the source code for the direct implementation: > > http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-pysrc.html > > Trelax is the 'relax_time' argument here. You can find all > implementation details in this API documentation. Which relaxation > time would you suggest as being correct? I'm actually no longer sure > which is being used. And I'm not sure if the original code or even > the numeric model itself was designed to handle variable time data. > > >> Maybe I am the minority to use such time consuming experiments, so I always >> have such strange questions ... > > relax should still handle the situation. Do you know if there is a > special treatment for the numerical models for such data? Do you know > of a good citation? Maybe the 'NS R1rho 2-site' model > (http://wiki.nmr-relax.com/NS_R1rho_2-site) is not suitable for > variable time data, and a different - and importantly published - > solution is required. The analytic models do not use the relaxation > time value, so those are safe. Hence, as a check, you should see very > similar results from the 'DPL94' model > (http://wiki.nmr-relax.com/DPL94) and the 'NS R1rho 2-site' model. If > not, something is wrong. > > If the 'NS R1rho 2-site' model is really only for fixed-time data, > then we should modify relax to raise a RelaxError when this model is > chosen for optimisation and the data is variable time. As not many > people optimise numeric models to variable-time data, your input into > this question would be very valuable. Cheers! > > >> Maybe another annoying question for the fix time people: >> Another question, does it necessary to check how mono-exponential about >> their relaxation curve under certain rf-field? If not, how did they make >> sure they can use the mono-exponential assumption to get R2eff by two points? > > From what I've seen and heard, some people do check, but the majority > just assume that the curves will be mono-exponential and publish the > fixed-time data and results. Such a check is probably much more > important for those collecting R1rho-type data rather than CPMG-type > data. Anyway, maybe you should ask people in front of their posters > at conferences to get a better overview of what the field does. > > Regards, > > Edward > > >> >> Best, >> >> 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. _______________________________________________ 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
