Re: relax_fit problem

[Edward d'A. <ed...@do...>]

Hi,

Not a problem.  Don't hesitate to ask if you have any other problems.
And thank you for the bug report, in new versions of relax the
warnings from reading a NMRView peak list will now make more sense.

Cheers,

Edward



On 9 March 2011 17:45, Elio Cino <her...@do...> wrote:
> I think I have it working now. I resolved it by uncommenting the
> spectrum.baseplane_rmsd line and removing the spin_id part of that
> command. I knew it was something simple to do with using the new
> script compared to the old one. Thanks for your help.
>
> On Wed, Mar 9, 2011 at 11:12 AM, Edward d'Auvergne <ed...@do...> wrote:
>> Hi,
>>
>> relax will run fine without these peaks included.  I have modified
>> relax to print out more meaningful warnings when unassigned NMRView
>> peaks are encountered.  The problem looks like there is another issue.
>>  Would you be able to attach all the NMRView peak lists?  But please
>> delete all but the first two assignment lines in each.  Do you see an
>> error message?  Could you run your analysis again, but on the
>> truncated NMRView files?  Does it work if you uncomment the baseplane
>> RMSD user function?
>>
>> Regards,
>>
>> Edward
>>
>>
>> On 9 March 2011 16:59, Elio Cino <her...@do...> wrote:
>>> I realize that those peaks are not labelled. They were unassigned
>>> residues. In the previous version I used 1.3.3 I had many unlabeled
>>> peaks and there was not any problem running relax. Do I need to remove
>>> these lines from the xpk in order to get relax working now? My problem
>>> is that relax seems to abort and I do not get any of the relaxation
>>> data output, just blank files.
>>>
>>> On Wed, Mar 9, 2011 at 5:53 AM, Edward d'Auvergne <ed...@do...> wrote:
>>>> Hi,
>>>>
>>>> Unfortunately this print out information is not enough for me to
>>>> determine what the problem is.  The problem could be earlier when you
>>>> read in the sequence.  If you could submit a bug report, that would be
>>>> much appreciated (https://gna.org/bugs/?func=additem&group=relax).  If
>>>> you could include the full print out from relax, the information you
>>>> get from typing 'relax --info', your script, the sequence file, and
>>>> the 500.xpk file, it would be much appreciated and I should be able to
>>>> then fix the problem in a few minutes.  If you would like to keep the
>>>> data confidential, you could remove all but the first 2 peaks from the
>>>> 500.xpk file (and the sequence file), and even randomise the value of
>>>> the peak height.  Essentially if I have a tiny randomised data set and
>>>> relax script which demonstrates the bug, I would add this to the relax
>>>> test suite.  That will allow me to debug it in a few minutes and also
>>>> to ensure that this data will be readable for the lifetime of relax.
>>>>
>>>> Cheers,
>>>>
>>>> Edward
>>>>
>>>>
>>>>
>>>> On 8 March 2011 21:59, Elio Cino <her...@do...> wrote:
>>>>> Hello. I have not used relax in a while and upgraded to the latest
>>>>> 1.3.10 before doing my curve fitting. I am having a problem with the
>>>>> sample script and have pasted a bit out the output below. I am not
>>>>> sure what is going on here. Any help is appreciated. Thanks.
>>>>>
>>>>> Opening the file '500.xpk' for reading.
>>>>> NMRView formatted data file.
>>>>>
>>>>> Number of header lines: 6
>>>>> Using peak heights.
>>>>> RelaxWarning: Cannot find the spin :@ within the sequence.
>>>>> RelaxWarning: Cannot find the spin :@ within the sequence.
>>>>> RelaxWarning: Cannot find the spin :@ within the sequence.
>>>>>
>>>>>
>>>>> --
>>>>> Elio Cino
>>>>>
>>>>> _______________________________________________
>>>>> relax (http://nmr-relax.com)
>>>>>
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>>>>
>>>
>>>
>>>
>>> --
>>> Elio Cino
>>>
>>
>
>
>
> --
> Elio Cino
>