On Wed, Apr 2, 2008 at 7:11 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:
Hi,
I tried to use the palmer.extract() function, with no real success...
I have to admit that my Modelfree star format parser is not of very
high quality. It woks if you use the palmer.py sample script, but
obviously not in this situation. Nothing that's not fixable though.
I'll start a new thread about this in the relax-devel mailing list.
I had several error message during my first tries and manage to get rid of
them with a script like :
=======================================
runs = ['m1', 'm2', 'm3', 'm4', 'm5']
diff_tensor_Phi = 22.4
diff_tensor_Theta = -3.49
diff_tensor_Dratio = 1.22
diff_tensor_tm = 1.242e-08
for name in runs:
run.create(name, 'mf')
sequence.read(name, 'sequence')
diffusion_tensor.init(name, (diff_tensor_tm, diff_tensor_Dratio,
diff_tensor_Theta, diff_tensor_Phi), param_types=2, spheroid_type='prolate',
fixed=1)
palmer.extract(run=name)
name = 'aic'
run.create(name, 'mf')
sequence.read(name, 'sequence')
relax_data.read(name, 'R1', '800', 799.812 * 1e6,
'800_R1.dat_plus_sequence')
relax_data.read(name, 'R2', '800', 799.812 * 1e6,
'800_R2.dat_plus_sequence')
relax_data.read(name, 'R1', '600', 599.739 * 1e6,
'600_R1.dat_plus_sequence')
relax_data.read(name, 'R2', '600', 599.739 * 1e6,
'600_R2.dat_plus_sequence')
relax_data.read(name, 'NOE', '600', 599.739 * 1e6,
'600_NOE.dat_plus_sequence')
relax_data.read(name, 'R1', '500', 499.827 * 1e6,
'500_R1.dat_plus_sequence')
relax_data.read(name, 'R2', '500', 499.827 * 1e6,
'500_R2.dat_plus_sequence')
relax_data.read(name, 'NOE', '500', 499.827 * 1e6,
'500_NOE.dat_plus_sequence')
diffusion_tensor.init(name, (diff_tensor_tm, diff_tensor_Dratio,
diff_tensor_Theta, diff_tensor_Phi), param_types=2, spheroid_type='prolate',
fixed=1)
model_selection(method='AIC', modsel_run=name)
results.write(run=name, file='results', force=1)
=======================================
It is a little strange that you need to read in the sequence and the
relaxation data for the 'aic' run. If you look at the palmer.py
sample script in the exec_stage_2() function, you'll see that none of
this is done. The following should also work:
=======================================
runs = ['m1', 'm2', 'm3', 'm4', 'm5']
diff_tensor_Phi = 22.4
diff_tensor_Theta = -3.49
diff_tensor_Dratio = 1.22
diff_tensor_tm = 1.242e-08
for name in runs:
run.create(name, 'mf')
sequence.read(name, 'sequence')
diffusion_tensor.init(name, (diff_tensor_tm, diff_tensor_Dratio,
diff_tensor_Theta, diff_tensor_Phi), param_types=2,
spheroid_type='prolate', fixed=1)
The rest of the setup user functions ....
palmer.extract(run=name)
name = 'aic'
run.create(name, 'mf')
model_selection(method='AIC', modsel_run=name)
results.write(run=name, file='results', force=1)
=======================================
However, there is one problem still present : no model is chosen during AIC
selection... Here is what I get after the command
"model_selection(method='AIC', modsel_run=name)" :
=======================================
...
Instance 261.
Run Num_params_(k) Num_data_sets_(n) Chi2
Criterion
The model from the run None has been selected.
...
=======================================
Is this for all spins? Maybe running relax with the --debug flag will
give more information.
It seems the mfout (which are all located in their respective folder : m1,
m2 , m3, m4 and m5) are not loaded properly...
Do you have any clue about this issue ?
Sorry, I don't have any idea. This will require investigation of the
relax data storage object to see what data is loaded from the mfout
file, and quite likely a little bit of coding, if you wish to do so.
Please refer to my post to relax-devel which will come soon.
Also, is there a way of extracting information from a mfout with relax
without inputing any sequence, diffusion tensor, or data..? I thought it
would be possible to use palmer.extract() in a short script like this :
=======================================
runs = ['m1', 'm2', 'm3', 'm4', 'm5']
for name in runs:
palmer.extract(run=name)
name = 'aic'
run.create(name, 'mf')
model_selection(method='AIC', modsel_run=name)
results.write(run=name, file='results', force=1)
=======================================
Do you see anything I do wrong ?
There is nothing wrong, the mfout file parser doesn't yet extract this
information. I'll continue this in my post to relax-devel.
Cheers,
Edward
Re: AIC from ModeFree data