Greetings,
I have encountered a problem running the script full_analysis.py
using v1.3.2 of relax (and python v2.5). I am currently executing
the script with the MI option (DIFF_MODEL = local_tm). I find that
the script successfully reads in data files and carries out the grid
search and minimization specified under the multi_model function for
the very first tm0 model. However, it appears that there is a
problem executing the final command of the function writing the
results to an output file (see reproduction of log file and traceback
below). The proper directory and file are created, but the results
file remains empty; and the script returns the error message
'IndexError: list index out of range'.
I obtain the same error using various formatted versions of my own
data files, as well as the test data files found in
/test_suite/shared_data/model_free/S2_0
.0.149/, modified to include
None for data values of GLY 1. Running multi_model commands manually
through the relax prompt also returns the same error for both
'results.write' and 'results.display.' I also obtain the same result
running the analysis with sample_scripts/model-free.py.
I am new to python and the relax interface and apologize if I am
bringing up a very basic question. I appreciate any help and
suggestions you might have. Thanks!
Regards,
Chris
Log File (edited)
relax> pipe.create(pipe_name='tm0', pipe_type='mf')
relax> sequence.read(file='noe.500.out',
dir='~/relax/relax-1.3.2/sample_scripts/data', mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None,
sep=None)
Opening the file
'/home/broseyca/relax/relax-1.3.2/sample_scripts/data/noe.500.out'
for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 ALA None None
relax> relax_data.read(ri_label='R1', frq_label='500',
frq=500100000.0, file='r1.500.out',
dir='~/relax/relax-1.3.2/sample_scripts/data', mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None,
data_col=2, error_col=3, sep=None)
Opening the file
'/home/broseyca/relax/relax-1.3.2/sample_scripts/data/r1.500.out' for
reading.
#(A total of 6 relaxation files were read in).
relax> model_free.select_model(model='tm0', spin_id=None)
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
relax> minimise(*args=('newton',), func_tol=1e-25,
max_iterations=10000000, constraints=True, scaling=True, verbosity=1)
relax> results.write(file='results', dir='local_tm/tm0', force=True,
format='xml', compress_type=1)
Opening the file 'local_tm/tm0/results.bz2' for writing.
Traceback Message
77 sweet:/home/broseyca/relax/relax-1.3.2% Traceback (most recent call last):
File "relax", line 410, in <module>
Relax()
File "relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line
270, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line
531, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line
427, in interact_script
execfile(script_file, local)
File "prompt/full_analysis2.py", line 668, in <module>
Main(self.relax)
File "prompt/full_analysis2.py", line 221, in __init__
self.multi_model(local_tm=True)
File "prompt/full_analysis2.py", line 664, in multi_model
results.write(file='results', dir=dir, force=True)
File "/home/broseyca/relax/relax-1.3.2/prompt/results.py", line 173,
in write
results.write(file=file, directory=dir, force=force,
format=format, compress_type=compress_type)
File "/home/broseyca/relax/relax-1.3.2/generic_fns/results.py", line
164, in write
write_function(results_file)
File "/home/broseyca/relax/relax-1.3.2/data/__init__.py", line 222,
in to_xml
self[self.current_pipe].to_xml(self.xmldoc, pipe_element)
File "/home/broseyca/relax/relax-1.3.2/data/pipe_container.py", line
234, in to_xml
self.mol.to_xml(doc, element)
File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line
690, in to_xml
self[i].res.to_xml(doc, mol_element)
File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line
492, in to_xml
self[i].spin.to_xml(doc, res_element)
File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line
242, in to_xml
desc = return_data_desc(name, spin=self[i])
File
"/home/broseyca/relax/relax-1.3.2/specific_fns/model_free/main.py",
line 2082, in return_data_desc
rex_units = self.return_units('rex', spin=spin)
File
"/home/broseyca/relax/relax-1.3.2/specific_fns/model_free/main.py",
line 2285, in return_units
return spin.frq_labels[0] + ' MHz'
IndexError: list index out of range