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/S2
0.149, 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
<[EMAIL PROTECTED]> 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/S2
0.149, 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 ':[EMAIL PROTECTED]'.
> Extracted N-H vectors for ':[EMAIL PROTECTED]'.
> Extracted N-H vectors for ':[EMAIL PROTECTED]'.
> Extracted N-H vectors for ':[EMAIL PROTECTED]'.
>
> 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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