Re: RelaxError: Grid search size too large? -- November 17, 2008

Hi,

This one again is an obvious bug.  I should be able to add this to the
system test that caught the other 2 bugs you found.  I have a feeling
that the problem will occur for the test files from
/test_suite/shared_data/model_free/S20.149, just that the error isn't
triggered.  The previous fix() user function should have deselected
all spins so that only the diffusion tensor is optimised.  However
this is not happening for some reason.  If you could file a bug report
for this too, that would be much appreciated.  That way anyone else
who encounters the bug can find it in the bug tracker.

Cheers,

Edward



On Thu, Nov 13, 2008 at 6:44 PM, Brosey, Chris A
<chris.a.brosey@xxxxxxxxxxxxxx> wrote:

Greetings,

I have moved on to running the full_analysis.py script for the 'sphere'
model and am encountering an error in the size of the grid search for the
diffusion tensor (see traceback and output logs below).  I am using
experimental input data of my own (~246 residues) that has been formatted to
match the test files that I have used previously.  The only alteration to
the script after a successful 'local_tm' run was to specify 'sphere' as the
diffusion model.  This error does not occur when I run the test files from
/test_suite/shared_data/model_free/S20.149, so I am not sure what is going
on.  The reference pdb I am using is the output of the Palmer r2r1_diffusion
script.

As always, I appreciate any help or suggestions you might have to offer.
Enjoy a great morning!

Best regards,

Chris

Log File (edited)

relax> pipe.create(pipe_name='sphere', pipe_type='mf')

relax> results.read(file='results', dir='local_tm/aic')
Opening the file 'local_tm/aic/results' for reading.

relax> model_free.remove_tm(spin_id=None)

relax>
structure.read_pdb(file='~/relax/relax-1.3.2/relax-1.3/sample_scripts/data/1fgu_mfdiffusion.pdb',
dir=None, model=None, parser='scientific')

Scientific Python PDB parser.
Loading all structures from the PDB file.
Structure('/home/broseyca/relax/relax-1.3.2/relax-1.3/sample_scripts/data/1fgu_mfdiffusion.pdb'):
  Peptide chain of length 246

relax> structure.vectors(attached='H', spin_id=None, struct_index=None,
verbosity=1, ave=True, unit=True)
Extracting vectors from the single structure.
Calculating the unit vectors.
The attached atom is a proton.

Extracted N-H vectors for ':187@N'.
Extracted N-H vectors for ':190@N'.
Extracted N-H vectors for ':193@N'.
Extracted N-H vectors for ':194@N'.

relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=False)

relax> fix(element='all_spins', fixed=True)

relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
The diffusion tensor parameters together with the model-free parameters for
all spins will be used.
Unconstrained grid search size:
103535780163953945786013051631026572323548694215165037063459636004169686022181124545004627721606706571L
(constraints may decrease this size).

relax> state.save(state='relax_state_20081311_102400', dir_name=None,
force=False, compress_type=1)
Opening the file 'relax_state_20081311_102400.bz2' for writing.

Traceback Log

66 sweet:/home/broseyca/relax/relax-1.3.2/relax-1.3% Traceback (most recent
call last):
  File "sample_scripts/full_analysis2.py", line 665, in <module>
    Main(self.relax)
  File "sample_scripts/full_analysis2.py", line 276, in __init__
    grid_search(inc=inc)
  File "/home/broseyca/relax/relax-1.3.2/relax-1.3/prompt/minimisation.py",
line 156, in grid_search
    minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
  File "/home/broseyca/relax/relax-1.3.2/relax-1.3/generic_fns/minimise.py",
line 185, in grid_search
    grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
  File
"/home/broseyca/relax/relax-1.3.2/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 479, in grid_search
    self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
  File
"/home/broseyca/relax/relax-1.3.2/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 921, in minimise
    min_options = self.grid_search_config(num_params, spin=spin,
lower=lower, upper=upper, inc=inc, scaling_matrix=scaling_matrix)
  File
"/home/broseyca/relax/relax-1.3.2/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 551, in grid_search_config
    self.test_grid_size(min_options, verbosity=verbosity)
  File
"/home/broseyca/relax/relax-1.3.2/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 1321, in test_grid_size
    raise RelaxError, "A grid search of size " + `grid_size` + " is too
large."
RelaxError: RelaxError: A grid search of size
103535780163953945786013051631026572323548694215165037063459636004169686022181124545004627721606706571L
is too large.


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Re: RelaxError: Grid search size too large?

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