For the sequence input file I think you want Spin_Name to be N if this is 15N
relaxation data. I'm also thinking it's not a bad idea to update to the latest
build of relax using subversion (can easily find/download this software via
google). This looks vaguely similar to some of the problems Edward had
debugged
for me, so probably worth the time to update if you're going to use this
script.
The command to execute in the relax directory would be:
svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3
And then a newer version of relax is put in a nested folder in the relax
directory. You want to make sure that the system path refers to the
newer build
of relax instead of the one you originally downloaded. When you type
'relax' it
should say something like 'system repository checkout' instead of 'relax
1.3.2.'
So the new directory would be ../relax-1.3.2/relax-1.3
Edward will probably have a more effective response, but this stuff will
probably prevent other problems in any case.
Tyler
Quoting "Brosey, Chris A" <[EMAIL PROTECTED]>:
> 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
>
>
>
>
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