Hi Leanne,
I've added your randomised, truncated data to the relax test suite,
but the test passes! The peak lists attached to the bug report
(https://gna.org/bugs/index.php?17276) are perfectly fine and do not
trigger the bug. From the full data set (sent in a private email for
confidentiality), I can see that the problem is because the entries in
the peak lists are not in the same order. If I look at the first 4
lines of a subset of the peak lists, I see:
[e...@localhost T1_relax]$ cat T10102done.list T1010done.list
T112002done.list T11200done.list
Assignment w1 w2 Intensity
A1649N-HN xx xx xx
D1514N-HN xx xx xx
Assignment w1 w2 Intensity
A1649N-HN xx xx xx
R1615N-HN xx xx xx
Assignment w1 w2 Intensity
A1649N-HN xx xx xx
D1514N-HN xx xx xx
Assignment w1 w2 Intensity
A1649N-HN xx xx xx
R1615N-HN xx xx xx
This is enough to trigger the bug. I will change half the 'R1615N-HN'
entries to 'D1514N-HN' to catch the bug. I would like relax to be
able to handle this data without issue, maybe warning that the peak
lists are not synchronised but still handling the residual data, but a
quick fix would be to sort out your peak lists.
Cheers,
Edward
On 3 December 2010 11:15, Edward d'Auvergne <[email protected]> wrote:
> Dear Leanne,
>
> Welcome to the relax mailing lists. The error you have found seems to
> be from a new bug in relax. I don't think anyone has encountered this
> one before. It would be very much appreciated if you could report
> this within the relax bug tracker
> (https://gna.org/bugs/?func=additem&group=relax). This would allow
> others who encounter the same problem to find out what is happening.
> And it will also help me in debugging the issue, as input files, test
> data, etc. can be attached to the bug report. If you could come up
> with a minimal set of test data (truncated, and randomised if you wish
> to hide the data) along with a script that reproduces the bug, I
> should be able to have a fix within a few minutes. With the current
> information you sent, it is very, very difficult for me to pinpoint
> the location of the problem.
>
> Cheers,
>
> Edward
>
>
>
> On 1 December 2010 15:54, L Minall <[email protected]> wrote:
>> Dear All,
>>
>> I am using Relax ( version relax-1.3.5.GNU-Linux) to get relaxation curves
>> from HSQC spectra. I have exported the data from analysis in Sparky
>> format. After running for a few seconds i get he following error message
>> 'List Index out of Range'.
>>
>> Below is a print screen of the problem:
>>
>>
>> relax> spectrum.replicated(spectrum_ids=['T11000done', 'T110002done'])
>>
>> relax> spectrum.replicated(spectrum_ids=['T11200done', 'T112002done'])
>>
>> relax> spectrum.error_analysis()
>> Intensity measure: Peak heights.
>> Replicated spectra: Yes.
>> All spectra replicated: Yes.
>>
>> Replicated spectra: ['T1010done', 'T10102done']
>> Standard deviation: 77677.6124466
>>
>> Replicated spectra: ['T1020done', 'T10202done']
>> Standard deviation: 81714.9935075
>>
>> Replicated spectra: ['T1030done', 'T10302done']
>> Standard deviation: 52174.0074096
>>
>> Replicated spectra: ['T1050done', 'T10502done']
>> Standard deviation: 101149.864468
>>
>> Replicated spectra: ['T1070done', 'T10702done']
>> Standard deviation: 59278.6902247
>>
>> Replicated spectra: ['T1100done', 'T11002done']
>> Standard deviation: 41827.710636
>>
>> Replicated spectra: ['T1150done', 'T11502done']
>> Standard deviation: 70130.6742832
>>
>> Replicated spectra: ['T1200done', 'T12002done']
>> Standard deviation: 80696.9386138
>>
>> Replicated spectra: ['T1300done', 'T13002done']
>> Standard deviation: 75574.7377343
>>
>> Replicated spectra: ['T1400done', 'T14002done']
>> Standard deviation: 109708.032792
>>
>> Replicated spectra: ['T1600done', 'T16002done']
>> Standard deviation: 96472.7940924
>>
>> Replicated spectra: ['T1800done', 'T18002done']
>> Standard deviation: 78680.8879662
>>
>> Replicated spectra: ['T11000done', 'T110002done']
>> Standard deviation: 263613.329907
>>
>> Replicated spectra: ['T11200done', 'T112002done']
>> Traceback (most recent call last):
>> File "/home/ms4225/programs/relax-1.3.5/relax", line 358, in <module>
>> Relax()
>> File "/home/ms4225/programs/relax-1.3.5/relax", line 126, in __init__
>> self.interpreter.run(self.script_file)
>> File "/home/ms4225/programs/relax-1.3.5/prompt/interpreter.py", line
>> 287, in run
>> return run_script(intro=self.__intro_string, local=locals(),
>> script_file=script_file, quit=self.__quit_flag,
>> show_script=self.__show_script,
>> raise_relax_error=self.__raise_relax_error)
>> File "/home/ms4225/programs/relax-1.3.5/prompt/interpreter.py", line
>> 533, in run_script
>> return console.interact(intro, local, script_file, quit,
>> show_script=show_script, raise_relax_error=raise_relax_error)
>> File "/home/ms4225/programs/relax-1.3.5/prompt/interpreter.py", line
>> 429, in interact_script
>> execfile(script_file, local)
>> File "R1_newLM.py", line 125, in <module>
>> spectrum.error_analysis()
>> File "/home/ms4225/programs/relax-1.3.5/prompt/spectrum.py", line 221,
>> in error_analysis
>> spectrum.error_analysis()
>> File "/home/ms4225/programs/relax-1.3.5/generic_fns/spectrum.py", line
>> 394, in error_analysis
>> __errors_repl()
>> File "/home/ms4225/programs/relax-1.3.5/generic_fns/spectrum.py", line
>> 189, in __errors_repl
>> ave_intensity = ave_intensity + spin.intensities[indices[j]]
>> IndexError: list index out of range
>>
>> Could anyone point me in the direction of finding this error, as it the
>> message seems a bit ambiguous?
>>
>> Many Thanks
>>
>> Leanne
>>
>>
>>
>>
>> --
>>
>>
>> --
>>
>>
>>
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>>
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