Hi Paul, For the literature data, which paper did you choose? Are you asking Dmitry Korzhnev about his 2004 JACS paper (http://dx.doi.org/10.1021/ja049968b)? Having both the base data, ideally in peak list form, together with the fitted parameters or original parameters for simulated data would be great. I would like to create a relax system test which analyses the SQ + MQ CPMG data simultaneously, and then I would write the code to make the test pass.
Cheers, Edward On 4 September 2013 20:30, Paul Schanda <[email protected]> wrote: > Hi Edward, > > I managed to find some literature data that are probably suitable. I will > get them from the authors in a week or so. > So that probably solves point 3). > > I agree that the infrastructure needs to be revised for MQ data. This might > in fact be the opportunity to re-think the structure. One might want to > jointly fit all kinds of data, e.g. SQ+MQ, or CPMG+R1rho. You should also > think of the possibility of adding in the future EXSY data. In the slow to > intermediate exchange, one might have EXSY + CPMG to be fit together. > If relax would be designed now in a way that is sufficiently flexible to > handle all this, it would be great. > > We will have a look at the code that Mathilde and Dominique have > implemented; this might also take a few days. > > best - > > > Paul > > > On 04.09.13 16:47, Edward d'Auvergne wrote: >> >> The following are reference development notes for how to modify relax >> to handle multi-quantum (MQ) data. Currently relax supports >> single-quantum (SQ) data but not MQ data. There are three aspects to >> this problem, detailed below. Note that the changes for part 2) will >> likely break the code of the relax_disp branch for a short time. >> >> >> 1) The MQ models. >> >> Firstly the specific MQ model(s) must be added to relax (following the >> steps at >> http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax). >> This part is relatively trivial, especially if the code already >> exists, a published reference exists, and equations can be copied from >> a paper directly into the relax manual. For example the 'MQ CR72' >> model supported by GUARDD (http://dx.doi.org/10.1021/ja049968b). >> >> >> 2) Infrastructure changes. >> >> There is one infrastructure change required to support this. The >> reason is because most people with MQ data will want to analyse it >> simultaneously with SQ data (well, that is my guess from the >> literature data). Support for optimising both SQ and MQ data >> simultaneously needs to be added. Currently relax only handles one >> type of dispersion data per data pipe. This should not be too hard to >> change. Such a change could allow CPMG-type and R1rho-type data to be >> analysed simultaneously as well. In each individual data combination >> case, a specific combined model such as 'SQ+MQ CR72' would need to be >> created. This model would be independent of the 'CR72' and 'MQ CR72' >> models, and the user will have to explicitly select it. >> >> The only change from the perspective of the user would the >> relax_disp.exp_type user function. This user function currently sets >> the experiment type for all data in the current data pipe. This needs >> to be changed to be similar to the relax_disp.cpmg_frq, >> relax_disp.relax_time, relax_disp.spin_lock_field, etc user functions, >> where the experiment type is associated with a spectrum ID. The GUI >> would be changed so that this user function is not presented when >> setting up a new analysis, but rather when the peak lists are being >> loaded. The GUI element displaying the experiment type would need to >> be removed and the data presented in the peak list GUI element >> instead. >> >> The backend changes would be more extensive. The following generator >> functions would need to be added to >> specific_analyses.relax_disp.disp_data: >> >> loop_exp() - for new usages. >> loop_exp_frq() - to replace calls to loop_frq(). >> loop_exp_frq_point() - to replace calls to loop_frq_point(). >> loop_exp_frq_point_time() - to replace calls to loop_frq_point_time(). >> >> The the code in specific_analyses.relax_disp and >> target_functions.relax_disp need to be modified around this new >> concept. I.e. a new top level looping needs to be inserted. The >> looping hierarchy from highest level to lowest would become: >> experiment type, magnetic field strength, dispersion point (CPMG >> frequency or spin-lock field strength), and finally relaxation time. >> The only difference to now is the highest level experiment type >> looping. >> >> The cdp.exp_type data structure will need to be converted into a >> dictionary where the keys are the spectrum IDs. >> >> >> 3) Test data. >> >> More of an issue is data! Test data is essential to be sure that the >> code is functional. And in relax it needs to be incorporated into a >> system test. The most important point is that the data needs to be >> independent of relax - the same code for fitting cannot be used to >> generate synthetic data. The more independence between relax and this >> test data, the better. >> >> Literature data for MQ data appears not to be available. It looks >> like corresponding authors would need to be emailed for access to the >> base data and numerical results. An alternative is provided by the >> Matlab software GUARDD. It has a module for simulating dispersion >> data >> (http://code.google.com/p/guardd/#Optimization_and_education_with_RD_Simulator). >> This could be used to generate the test data to be included with >> relax. Some test data is also provided by the program. This could >> also be used, but it suffers from the fact that the real parameter >> values are not known. But it can be used to directly compare relax >> and GUARDD. >> >> Regards, >> >> Edawrd >> > > > -- > Paul Schanda, Ph.D. > Biomolecular NMR group > Institut de Biologie Structurale Jean-Pierre Ebel (IBS) > 41, rue Jules Horowitz > F-38027 Grenoble > France > +33 438 78 95 55 > [email protected] > http://www.ibs.fr/groups/biomolecular-nmr-spectroscopy?lang=en > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] 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-devel
