In the relax prompt, this can produce the error:
---------------------
pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx')
relax_disp.exp_type(exp_type='cpmg fixed')
sequence.read(file='/sbinlab2/tlinnet/Desktop/test.seq',
dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
spin_id=None)
spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/test.seq',
dir=None, spectrum_id=(2,0), heteronuc='N', proton='HN',
int_method='height', int_col=(6, 7), spin_id_col=None, mol_name_col=1,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5,
sep=None, spin_id=None, ncproc=None)
File "<input>", line 3, in <module>
File "/sbinlab2/software/NMR-relax/relax_disp/prompt/uf_objects.py",
line 200, in __call__
lib.arg_check.is_str(value, desc_short, can_be_none=can_be_none)
File "/sbinlab2/software/NMR-relax/relax_disp/lib/arg_check.py",
line 862, in is_str
raise RelaxStrError(name, arg)
RelaxStrError: [31mRelaxError: The spectrum ID string argument '(2,
0)' must be a string. [0m
-----------------------------------------
2013/6/6 Edward d'Auvergne <edw...@nmr-relax.com>:
> On a different note, if you notice anywhere in relax's execution where
> the messages are not informative enough, are misleading, or where
> additional messages would be useful, these can all be reported as
> bugs. Anything in relax that causes confusion should be considered a
> bug which should be fixed.
>
> Regards,
>
> Edward
>
>
>
> On 6 June 2013 15:26, Edward d'Auvergne <edw...@nmr-relax.com> wrote:
>> Oh, right, I see the problem. This user function currently only has
>> partial support for simultaneously loading all spectral data at once.
>> The current way to do this is to change the spectrum ID and intensity
>> column one-by-one while clicking on 'Apply' as you go. But I have
>> partly designed this user function to handle this situation, according
>> to the user function documentation:
>>
>> "Generic intensity file: This is a generic format which can be
>> created by scripting to support non-supported peak lists. It should
>> contain in the first few columns enough information to identify the
>> spin. This can include columns for the molecule name, residue number,
>> residue name, spin number, and spin name. Alternatively a spin ID
>> string column can be used. The peak intensities can be placed in
>> another column specified by the integration column number.
>> Intensities from multiple spectra can be placed into different
>> columns, and these can then be specified simultaneously by setting the
>> integration column value to a list of columns. This list must be
>> matched by setting the spectrum ID to a list of the same length..."
>>
>> Could you submit a bug report for this, attaching any files required
>> to replicate the bug? It would be useful to give a link to the Gmane
>> archive as well (going to
>> http://dir.gmane.org/gmane.science.nmr.relax.user -> clicking on
>> "using frames and threads" -> finding message -> clicking on "<<<
>> [thread] >>>" down the botton -> and copying the link). I could then
>> turn the instructions into a relax script, and incorporate both the
>> script and data files into the test suite directories and create a
>> system test to catch the bug. Or, if you wish, as a learning exercise
>> for becoming a relax developer you could give this a go yourself after
>> creating the report. This would all go into the relax trunk, and then
>> be ported to the relax_disp branch using svnmerge.py.
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>> On 6 June 2013 15:04, Troels Emtekær Linnet <tlin...@gmail.com> wrote:
>>> I think it is because that:
>>> spectrum_id='(2,6)'
>>>
>>> is translated to a string.
>>>
>>> Could it be corrected, so it does similar as:
>>> int_col=(6, 7)
>>>
>>> Best
>>> Troels Emtekær Linnet
>>>
>>>
>>> 2013/6/6 Troels Emtekær Linnet <tlin...@gmail.com>:
>>>> Hi,
>>>>
>>>> No, not any luck.
>>>> And, this time I am not renaming.
>>>>
>>>> Where can I find the longer error message?
>>>> ---------
>>>> Add spectra
>>>> Click "Add"
>>>>
>>>> The file name = test.seq
>>>> The Spectrum ID string: 2,0
>>>> The Intensity column: 6,7
>>>> ----------------
>>>> protein 10 L 10 N 3.377659e+05 6.362446e+05
>>>> protein 6 V 6 N 1.697771e+06 3.015788e+06
>>>> protein 63 Y 63 N 8.673898e+05 1.726064e+06
>>>> protein 4 Y 4 N 2.339480e+06 4.039142e+06
>>>> protein 67 M 67 N 2.574062e+06 4.313824e+06
>>>> protein 5 E 5 N 1.609356e+06 2.927111e+06
>>>> protein 65 V 65 N 2.179341e+06 4.067343e+06
>>>> protein 38 E 38 N 1.563795e+06 2.921316e+06
>>>> protein 7 N 7 N 1.535896e+06 3.005234e+06
>>>> protein 75 L 75 N 3.578841e+06 6.352595e+06
>>>> ------------------------
>>>>
>>>> ----------
>>>> relax> relax_disp.exp_type(exp_type='cpmg fixed')
>>>> The fixed relaxation time period CPMG-type experiments.
>>>>
>>>> relax>
>>>> sequence.read(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq',
>>>> dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2,
>>>> res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
>>>> spin_id=None)
>>>> Opening the file
>>>> '/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq'
>>>> for reading.
>>>> # mol_name res_num res_name spin_num spin_name
>>>> protein 10 L 10 N
>>>> protein 6 V 6 N
>>>> protein 63 Y 63 N
>>>> protein 4 Y 4 N
>>>> protein 67 M 67 N
>>>> protein 5 E 5 N
>>>> protein 65 V 65 N
>>>> protein 38 E 38 N
>>>> protein 7 N 7 N
>>>> protein 75 L 75 N
>>>>
>>>> relax>
>>>> spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq',
>>>> dir=None, spectrum_id='2,0', heteronuc='N', proton='HN',
>>>> int_method='height', int_col=(6, 7), spin_id_col=None, mol_name_col=1,
>>>> res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5,
>>>> sep=None, spin_id=None, ncproc=None)
>>>> Opening the file
>>>> '/sbinlab2/tlinnet/Desktop/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq'
>>>> for reading.
>>>> Generic formatted data file.
>>>>
>>>> RelaxWarning: The sequence data in the line ['protein', '10', 'L',
>>>> '10', 'N', '3.377659e+05', '6.362446e+05'] is invalid, the data is
>>>> missing.
>>>> RelaxWarning: The sequence data in the line ['protein', '6', 'V', '6',
>>>> 'N', '1.697771e+06', '3.015788e+06'] is invalid, the data is missing.
>>>> RelaxWarning: The sequence data in the line ['protein', '63', 'Y',
>>>> '63', 'N', '8.673898e+05', '1.726064e+06'] is invalid, the data is
>>>> missing.
>>>> RelaxWarning: The sequence data in the line ['protein', '4', 'Y', '4',
>>>> 'N', '2.339480e+06', '4.039142e+06'] is invalid, the data is missing.
>>>> RelaxWarning: The sequence data in the line ['protein', '67', 'M',
>>>> '67', 'N', '2.574062e+06', '4.313824e+06'] is invalid, the data is
>>>> missing.
>>>> RelaxWarning: The sequence data in the line ['protein', '5', 'E', '5',
>>>> 'N', '1.609356e+06', '2.927111e+06'] is invalid, the data is missing.
>>>> RelaxWarning: The sequence data in the line ['protein', '65', 'V',
>>>> '65', 'N', '2.179341e+06', '4.067343e+06'] is invalid, the data is
>>>> missing.
>>>> RelaxWarning: The sequence data in the line ['protein', '38', 'E',
>>>> '38', 'N', '1.563795e+06', '2.921316e+06'] is invalid, the data is
>>>> missing.
>>>> RelaxWarning: The sequence data in the line ['protein', '7', 'N', '7',
>>>> 'N', '1.535896e+06', '3.005234e+06'] is invalid, the data is missing.
>>>> RelaxWarning: The sequence data in the line ['protein', '75', 'L',
>>>> '75', 'N', '3.578841e+06', '6.352595e+06'] is invalid, the data is
>>>> missing.
>>>> RelaxError: No corresponding data could be found within the file.
>>>>
>>>> -------------------------------
>>>>
>>>> Troels Emtekær Linnet
>>>>
>>>>
>>>> 2013/6/6 Edward d'Auvergne <edw...@nmr-relax.com>:
>>>>> Hi,
>>>>>
>>>>> Have you had any luck finding the problem? I would guess that this
>>>>> doesn't work as the protein was renamed to something different to that
>>>>> of the data file, hence you would see messages such as:
>>>>>
>>>>> relax> spectrum.read_intensities(file='test.seq', dir=None,
>>>>> spectrum_id=None, heteronuc='N', proton='HN', int_method='height',
>>>>> int_col=6, spin_id_col=None, mol_name_col=1, res_num_col=2,
>>>>> res_name_col=3, spin_num_col=4, spin_name_col=5, int_col=6, sep=None,
>>>>> spin_id=None, ncproc=None)
>>>>> Opening the file '/data/edau/relax/branches/relax_disp/test.seq' for
>>>>> reading.
>>>>> Generic formatted data file.
>>>>>
>>>>> RelaxWarning: Cannot find the spin #protein:10@N within the sequence.
>>>>> RelaxWarning: Cannot find the spin #protein:6@N within the sequence.
>>>>> RelaxWarning: Cannot find the spin #protein:63@N within the sequence.
>>>>> RelaxWarning: Cannot find the spin #protein:4@N within the sequence.
>>>>> RelaxWarning: Cannot find the spin #protein:67@N within the sequence.
>>>>> RelaxWarning: Cannot find the spin #protein:5@N within the sequence.
>>>>> RelaxWarning: Cannot find the spin #protein:65@N within the sequence.
>>>>> RelaxWarning: Cannot find the spin #protein:38@N within the sequence.
>>>>> RelaxWarning: Cannot find the spin #protein:7@N within the sequence.
>>>>> RelaxWarning: Cannot find the spin #protein:75@N within the sequence.
>>>>> RelaxError: No data could be loaded from the peak list
>>>>>
>>>>> I tried this by copying the data in your post to a file and following
>>>>> the instructions. This is normal as the molecule with the name
>>>>> 'protein' no longer exists in the relax data store. Or did you see
>>>>> something different? The RelaxError text you wrote about is slightly
>>>>> different.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Edward
>>>>>
>>>>>
>>>>> On 4 June 2013 15:10, Edward d'Auvergne <edward.dauver...@gmail.com>
>>>>> wrote:
>>>>>> I have to admit, the error message should be made more informative!
>>>>>> However that error statement (line 668 of lib/io.py) cannot be reached
>>>>>> without relax giving many warnings. The only possibility of reaching
>>>>>> the error without warnings is if the file is empty. Do you see
>>>>>> warnings which could indicate the problem? If not, I would suggest
>>>>>> creating a bug report for the problem and attaching a minimal set of
>>>>>> files to be able to reproduce the issue. It would be best if the
>>>>>> files are truncated to 1-2 spins (and maybe randomised if the data is
>>>>>> to be kept secret). If it really is a bug, then these files could be
>>>>>> be added to the test suite and turned into a system or GUI test to
>>>>>> catch the problem.
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Edward
>>>>>>
>>>>>>
>>>>>> On 4 June 2013 14:37, Troels Emtekær Linnet <tlin...@gmail.com> wrote:
>>>>>>> Hi.
>>>>>>>
>>>>>>> I have made a custom intensity peak/model file, for easy import in
>>>>>>> relax.
>>>>>>> The form is:
>>>>>>>
>>>>>>> protein 10 L 10 N 3.377659e+05 6.362446e+05
>>>>>>> protein 6 V 6 N 1.697771e+06 3.015788e+06
>>>>>>> protein 63 Y 63 N 8.673898e+05 1.726064e+06
>>>>>>> protein 4 Y 4 N 2.339480e+06 4.039142e+06
>>>>>>> protein 67 M 67 N 2.574062e+06 4.313824e+06
>>>>>>> protein 5 E 5 N 1.609356e+06 2.927111e+06
>>>>>>> protein 65 V 65 N 2.179341e+06 4.067343e+06
>>>>>>> protein 38 E 38 N 1.563795e+06 2.921316e+06
>>>>>>> protein 7 N 7 N 1.535896e+06 3.005234e+06
>>>>>>> protein 75 L 75 N 3.578841e+06 6.352595e+06
>>>>>>>
>>>>>>> This goes fine for model import, with standard settings.
>>>>>>>
>>>>>>> Start new analysis
>>>>>>> Relaxation dispersion analysis
>>>>>>> Relaxation dispersion experiment type selection
>>>>>>> CPMG, fixed time
>>>>>>> Data pipe set up
>>>>>>> The starting data pipe for the analysis = origin - relax_disp (Mon Jun
>>>>>>> 3 17:08:30 2013)
>>>>>>> The data pipe bundle = relax_disp (Mon Jun 3 17:08:30 2013)
>>>>>>>
>>>>>>> Click: Spin editor
>>>>>>> Click: Load spins
>>>>>>> Make a test file: test.seq
>>>>>>>
>>>>>>> Click: From a file containing sequence data
>>>>>>> The file name = test.seq
>>>>>>> The spin ID string = Leave empty
>>>>>>> Free format
>>>>>>> Molecule name column (mol_name_col) = 1
>>>>>>> Residue number column (res_num_col) = 2
>>>>>>> Residue name column (res_name_col) = 3
>>>>>>> Spin number column (spin_num_col) = 4
>>>>>>> Spin name column (spin_name_col) = 5
>>>>>>> You can then rename molecule by, right click "Molecule: protein",
>>>>>>> "Name the molecule", Set "The new molecule name" to for example
>>>>>>> "Test". Apply, then OK.
>>>>>>>
>>>>>>> Add spectra
>>>>>>> Click "Add"
>>>>>>>
>>>>>>> The file name = test.seq
>>>>>>> The Spectrum ID string: 2,0
>>>>>>> The Intensity column: 6,7
>>>>>>> rest is default
>>>>>>>
>>>>>>> Error:
>>>>>>> No corresponding data could be found within the file.
>>>>>>>
>>>>>>> I can import single wise.
>>>>>>>
>>>>>>> best
>>>>>>> Troels
>>>>>>>
>>>>>>>
>>>>>>> Troels Emtekær Linnet
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> relax (http://www.nmr-relax.com)
>>>>>>>
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