I should mention, in fairness, that the minfx update I recently suggested may
not be necessary depending on your data, but still a decent idea to get the
fix.
Tyler
Quoting Edward d'Auvergne <[EMAIL PROTECTED]>:
> Cheers! That response pretty much covers it. I'm not sure if this is
> exactly the error I fixed for you Tyler, but I think the repository
> version doesn't have this problem. It would be useful to get the
> repository version anyway as then the debugged version will be
> instantly acessable by typing:
>
> $ svn up
>
> in the directory of the checked out copy. I can't guarantee a quick
> response time though as RSI in my wrist is slowing things down
> significantly - writing an email only with my left hand is hard
> enough, and debugging one handed would be a nightmare!
>
> Regards,
>
> Edward
>
>
> On Wed, Nov 5, 2008 at 8:03 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote:
>> 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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>
> _______________________________________________
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>
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>
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