Re: AIC from ModeFree dataRe: AIC from ModeFree data|
Hi, I tried to use the palmer.extract() function, with no real success... 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) ======================================= 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. ... ======================================= 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 ? 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 ? Thanks ! Séb :) Edward d'Auvergne wrote: Hi, This is simple enough to do. The user function palmer.extract() will extract all the data (well that used by relax) out of Modelfree's mfout files. Regards, Edward On Tue, Apr 1, 2008 at 11:41 PM, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:Hi, I have different model-free analysis that originated from the program ModelFree (with results in a 'mfout' file). I would like to know if there is a way of loading these data to proceed to model selection by AIC using relax. I there ain't any way of doing this, I'll turn to the palmer.py script and start from the beginning... Thanks ! Sébastien _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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 |