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
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