I ran the 1.2 version of the noe.py script with the 1.2 version of
relax on the
same machine and had a slightly different error output (below). If this is
simply a version-change problem with the script as you say, then I'm not sure
why I'd get a convoluted error with version 1.2 as well.
Output:
Calculating and averaging the unit XH vectors from all structures.
relax> noe.read(run='noe', file='NOnoe500.list', dir=None,
spectrum_type='ref',
format='sparky', heteronuc='N', proton='HN', int_col=None)
Reference spectrum.
Sparky formatted data file.
Opening the file 'NOnoe500.list' for reading.
Number of header lines found: 2
Traceback (most recent call last):
File "/Applications/relax-1.2.14/relax", line 457, in <module>
Relax()
File "/Applications/relax-1.2.14/relax", line 167, in __init__
self.interpreter.run()
File "/Applications/relax-1.2.14/prompt/interpreter.py", line 216, in run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File "/Applications/relax-1.2.14/prompt/interpreter.py", line 391, in
run_script
console.interact(intro, local, script_file, quit)
File "/Applications/relax-1.2.14/prompt/interpreter.py", line 343, in
interact_script
execfile(script_file, local)
File "noe_12.py", line 35, in <module>
noe.read(name, file='NOnoe500.list', spectrum_type='ref')
File "/Applications/relax-1.2.14/prompt/noe.py", line 226, in read
self.__relax__.specific.noe.read(run=run, file=file, dir=dir,
spectrum_type=spectrum_type, format=format, heteronuc=heteronuc,
proton=proton,
int_col=int_col)
File "/Applications/relax-1.2.14/specific_fns/noe.py", line 110, in read
self.relax.generic.intensity.read(run=run, file=file, dir=dir,
format=format, heteronuc=heteronuc, proton=proton, int_col=int_col,
assign_func=self.assign_function)
File "/Applications/relax-1.2.14/generic_fns/intensity.py", line 232, in read
res_num, H_name, X_name, intensity = self.intensity(self.file_data[i])
File "/Applications/relax-1.2.14/generic_fns/intensity.py", line 92, in
intensity_sparky
intensity = float(line[self.int_col])
IndexError: list index out of range
Quoting Edward d'Auvergne <[EMAIL PROTECTED]>:
> Hi,
>
> This is definitely a bug! If you could file a bug report
> (https://gna.org/bugs/?func=additem&group=relax), that would be much
> appreciated. If you would like a description of how this is done,
> please see section 3.3 of the relax manual (version 1.3) or the online
> HTML version (currently at
> http://www.nmr-relax.com/manual/1.3/node49.html).
>
> The reason this is failing is because this code in the 1.3 relax
> versions has not been converted to the new design yet. For me or the
> relax developers to implement this, first a system test should be
> added to the test suite. The test suite can be run by typing:
>
> $ relax --test-suite
>
> The system test is simply a very tiny, although complete, version of
> the analysis you would like to do. This can include a small subset of
> the base data, randomised if you'd like to protect the data prior to
> publication. With the small data subset, I can include your full
> analysis script into the test suite and execute it with the data.
> Then once the test passes, an NOE analysis will be possible. The data
> and script can be attached to the bug report. If you would like to
> help in getting this test implemented, that would be much appreciated.
>
> Thanks,
>
> Edward
>
>
>
> On Mon, Oct 6, 2008 at 3:31 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote:
>> Hello,
>>
>> I am having trouble with the noe.py script. I have peptide data with
>> 6 backbone
>> 15N labels, and I suspect it's a problem with input. I've tried several
>> permutations of full PDB file and full .list Sparky format files as well as
>> files trimmed down to include only the labeled residues. I'm not
>> sure which is
>> preferable/required for input, and if unlabeled residues can simply be left
>> with a blank column value or if there is a special way to treat this?
>>
>> Here is a sample of the output I get with any of my tries so far:
>>
>> Scientific Python PDB parser.
>> Loading all structures from the PDB file.
>> Structure('select.pdb'):
>> Peptide chain A of length 6
>>
>>
>> relax> structure.load_spins(spin_id='@N', ave_pos=True)
>> Adding the following spins to the relax data store.
>>
>> Mol_name Res_num Res_name Spin_num Spin_name
>> A 254 LEU 68 N
>> A 258 LEU 142 N
>> A 261 GLY 197 N
>> A 264 LEU 230 N
>> A 268 ALA 294 N
>> A 273 LEU 366 N
>>
>> relax> noe.read(file='NOnoe500_true.list', dir=None, spectrum_type='ref',
>> format='sparky', heteronuc='N', proton='HN', int_col=None)
>> Reference spectrum.
>> Traceback (most recent call last):
>> File "/Applications/relax-1.3.1/relax", line 408, in <module>
>> Relax()
>> File "/Applications/relax-1.3.1/relax", line 125, in __init__
>> self.interpreter.run(self.script_file)
>> File "/Applications/relax-1.3.1/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 "/Applications/relax-1.3.1/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 "/Applications/relax-1.3.1/prompt/interpreter.py", line 427, in
>> interact_script
>> execfile(script_file, local)
>> File "noe.py", line 36, in <module>
>> noe.read(file='NOnoe500_true.list', spectrum_type='ref')
>> File "/Applications/relax-1.3.1/prompt/noe.py", line 216, in read
>> noe_obj.read(file=file, dir=dir, spectrum_type=spectrum_type,
>> format=format,
>> heteronuc=heteronuc, proton=proton, int_col=int_col)
>> File "/Applications/relax-1.3.1/specific_fns/noe.py", line 114, in read
>> self.relax.generic.intensity.read(run=run, file=file, dir=dir,
>> format=format, heteronuc=heteronuc, proton=proton, int_col=int_col,
>> assign_func=self.assign_function)
>> AttributeError: Noe instance has no attribute 'relax'
>>
>>
>> _______________________________________________
>> relax (http://nmr-relax.com)
>>
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>>
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>>
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
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> [email protected]
>
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