Hi, Firstly I recommend you can change pA_value variable name to pA to match the notation used throughout the dispersion code. I would also add a new if statement for the kex to k_AB conversion to keep things separate and clean - it will make debugging easier for you. As for preventing the error, that cannot be done. This error is good and correct. The reason is because the implementation requires a number of changes to the specific_analyses.relax_disp.api module as well to be complete and functional - especially in the methods relating to the Monte Carlo simulations from where the spin.*_sim structures are created. You may encounter other errors, and this will simply indicate that more needs to be done. Grepping for the 'tex' and 'pB' auxiliary parameters will help you identify all possible locations where the support is required (only changes to specific_analyses.relax_disp are required).
Regards, Edward On 10 September 2013 11:44, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > I tried to modify parameters.py, so: > > ------------- > # The kex to tex conversion and kex to k_AB. > if param_name == 'kex': > tex = 1.0 / (2.0 * value) > set_value(value=tex, key=key, spins=spins, > sim_index=sim_index, param_name='tex', spin_index=spin_index, > frq_index=frq_index) > # Get pA value. > pA_value = get_value(key=key, spins=spins, > sim_index=sim_index, param_name='pA', spin_index=spin_index, > frq_index=frq_index) > k_AB = value * (1 - pA_value) > set_value(value=k_AB, key=key, spins=spins, > sim_index=sim_index, param_name='k_AB', spin_index=spin_index, > frq_index=frq_index) > ------------ > > But when an analysis of the CR72 model, I get this error: > > File > "/sbinlab2/tlinnet/software/NMR-relax/relax_disp/specific_analyses/relax_disp/api.py", > line 1179, in minimise > param_conversion(spins=spins, sim_index=sim_index) > File > "/sbinlab2/tlinnet/software/NMR-relax/relax_disp/specific_analyses/relax_disp/parameters.py", > line 721, in param_conversion > set_value(value=k_AB, key=key, spins=spins, sim_index=sim_index, > param_name='k_AB', spin_index=spin_index, frq_index=frq_index) > File > "/sbinlab2/tlinnet/software/NMR-relax/relax_disp/specific_analyses/relax_disp/parameters.py", > line 852, in set_value > sim_obj = getattr(spin, param_name+'_sim') > AttributeError: 'SpinContainer' object has no attribute 'k_AB_sim' > > How do I prevent this? > > Best > Troels > > > Troels Emtekær Linnet > > > 2013/9/9 Edward d'Auvergne <[email protected]>: >> Hi. >> >>> There is an explanation for everything, including user errors. :-) >> >> I'd call this more developer errors ;) Talking about development, I >> will soon ask the other relax developers about you joining the >> development team. This will have to wait a little while as I am on >> holidays for about 3 weeks starting from this weekend. >> >> >>> I have analysed the 0.48 M GuaHCl dataset (the folded protein), and so >>> this is not comparable to the >>> 1M GuaHcl (intermediate between folded/unfolded) dataset, which is >>> shown in the figures in the paper. >>> >>> So, I got the original datapoints for figure 3, which shows the >>> ln(k_a) per GuaHCl. >>> And now k_a fits perfect for 0.48 M. >>> >>> And I have today analysed the 1M dataset. >>> >>> Everything matches until first digit, so I am satisfied. >> >> This sounds great! The model is so incredibly simple that finding out >> that a data mix up was the source of the problem is quite a relief. >> >> >>> So, I will soon send a swarm of patches to include this dataset. >> >> All patched >> (http://thread.gmane.org/gmane.science.nmr.relax.devel/4372/focus=4563). >> >> >>> Thanks for looking! >>> >>> I will look into the tsmfk01 code to speed it up. >> >> No problems. I look forward to seeing your solutions. >> >> >>> To compare to the numerical methods, you mentioned that one could make >>> auto conversion of the >>> parameters? >>> >>> So could k_AB be calculated for the numerical methods, so: >>> k_AB = kex*(1-pA) >> >> Yes, this can be done. The complication is handling the Monte Carlo >> simulations, specifically the parameter error estimate calculation at >> the end of all simulations. You can have a go at this yourself, if >> you wish. The key is to look for where the 'tex' or 'pB' parameters >> are handled, as these are not parameters in most of the dispersion >> models, and to study this code. These two parameters will be handled >> as you wish k_AB to be. If k_AB is calculated, then so should k_BA. >> Maybe phi_ex should also be added to this list of 'auxiliary' >> parameters so that the numeric models can be easily compared to the >> fast exchange models. Are there any other auxiliary parameters you >> can think of? What about the alpha factor which determines if the >> exchange is fast, slow or intermediate? >> >> Cheers, >> >> Edward _______________________________________________ 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
