Re: Ellipsoid minimization does not converge -- May 17, 2010 - 19:22

Hi,

Wow, that's an incredible number of iterations!  Have you tried
Sebastien's consistency testing to see if there could be a problem
with the data?  The reference is in Seb's sample script that comes
with relax.  Is this a single domain protein?  As for this bug, I've
had a look at the code and it appears to be fixed in the repository.
Do you have the subversion program installed, and have you used it
before?  If so, you can download a copy of the repository code by
typing:

$ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3

or if this doesn't work:

$ svn co http://svn.gna.org/svn/relax/1.3 relax-1.3

If you already have a checked out copy, try typing:

$ svn up

in the base directory to update to the most current version.  If you
try this newest version, does this problem go away?

Regards,

Edward



2010/5/17 Daniel Pérez <daniel.perez@xxxxxxxxxxxxxxxx>:
> Hi everyone,
>
> Thanks Ed and Sébastien for your answers.
>
> The minimization with the ellipsoid tensor took good 31 rounds and finally 
> it passed the convergence test.
>
> Now I face anther issue, I couldn't make the program run through the model 
> selection. It crashes during the Monte Carlo simulation. Apparently it has 
> some trouble reading in the back calculated data.
>
> Here I attached the last steps before crashing
>
> I'll appreciate any feedback.
>
> Thanks in advance
>
> Daniel
>
>
>
> relax> monte_carlo.create_data(method='back_calc')
> Traceback (most recent call last):
>  File "/soft/group/relax/relax-1.3/relax", line 358, in ?
>    Relax()
>  File "/soft/group/relax/relax-1.3/relax", line 126, in __init__
>    self.interpreter.run(self.script_file)
>  File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 287, in run
>    return run_script(intro=self.__intro_string, local=locals(), 
> script_file=script_file, quit=self.__quit_flag, 
> show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
>  File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 533, in 
> run_script
>    return console.interact(intro, local, script_file, quit, 
> show_script=show_script, raise_relax_error=raise_relax_error)
>  File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 429, in 
> interact_script
>    execfile(script_file, local)
>  File "full_analysis_last.py", line 197, in ?
>    dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS, 
> local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS, 
> het_name=HET_NAME, relax_data=RELAX_DATA, unres=UNRES, exclude=EXCLUDE, 
> bond_length=BOND_LENGTH, csa=CSA, hetnuc=HETNUC, proton=PROTON, 
> grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_num=MC_NUM, conv_loop=CONV_LOOP)
>  File "/soft/group/relax/relax-1.3/auto_analyses/dauvergne_protocol.py", 
> line 401, in __init__
>    self.interpreter.monte_carlo.create_data()
>  File "/soft/group/relax/relax-1.3/prompt/monte_carlo.py", line 77, in 
> create_data
>    monte_carlo.create_data(method=method)
>  File "/soft/group/relax/relax-1.3/generic_fns/monte_carlo.py", line 69, in 
> create_data
>    data = create_mc_data(data_index)
>  File "/soft/group/relax/relax-1.3/specific_fns/model_free/main.py", line 
> 1175, in create_mc_data
>    value = self.back_calc_ri(spin_index=global_index, 
> ri_label=spin.ri_labels[j], frq_label=spin.frq_labels[spin.remap_table[j]], 
> frq=spin.frq[spin.remap_table[j]])
>  File "/soft/group/relax/relax-1.3/specific_fns/model_free/main.py", line 
> 452, in back_calc_ri
>    if hasattr(cdp, 'diff_tensor') and (cdp.diff_tensor.type == 'spheroid' 
> or cdp.diff_tensor.type == 'ellipsoid') and (not hasattr(spin, 'xh_vect') 
> or not spin.xh_vect):
> ValueError: The truth value of an array with more than one element is 
> ambiguous. Use a.any() or a.all()
>
>
>
> Dr. Daniel Pérez
> Institut für Molekularbiologie und Biophysik
> Schafmattstrasse 20
> ETH-Hönggerberg, HPK G 5
> CH-8093 Zürich
> Phone: +41 44 633 25 37
> E-mail: daniel.perez@xxxxxxxxxxxxxxxx
>
>
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