Sorry, please ignore and refrane from responding to this message. This one shouldn't have been sent - it's an old message in which all the technical parts were sent to the relax-devel mailing list.
Regards, Edward On Thu, Apr 3, 2008 at 5:44 PM, Edward d'Auvergne <[EMAIL PROTECTED]> wrote: > 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 > <[EMAIL PROTECTED]> 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 > > <[EMAIL PROTECTED]> 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 > > [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-users > > > > > > > > > > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users 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-users
