Hi, This post starts a new thread, but it follows on from the post at https://mail.gna.org/public/relax-users/2008-04/msg00005.html. The parent of the previous thread is located at https://mail.gna.org/public/relax-users/2008-04/msg00001.html. 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 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) 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. I think the 1.3 line would be best for any changes in this code. Almost all of the user functions you've used here have been updated to the new relax design and the rest should simply involve the removal of the run object from the relevant functions.
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 :
As of yet, no. The parser behind palmer.extract() will need to be significantly improved. The mfout file is STAR (Self Defining Text Archival and Retrieval) formatted. But the parser for this is very basic and hacky. If the mfout file is not as expected, palmer.extract() will fail. The star format is used in a number of other places as well. For example I plan to better incorporate relax with the BRMB (http://www.bmrb.wisc.edu) which uses the STAR format. And CIF files are also STAR formatted. So, ideally in the end I would like to create a STAR format writer and parser for relax. Or, if there is a STAR format reader already that is open source and can easily be imported into relax, then bundle that with relax. As far as I can tell, there is no official python package for reading and writing this format. But this will take time and will be very incremental. So if you would like to update the current code to read more of the mfout file details, please feel free. This STAR parser part in generic_fns/palmer.py
======================================= 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