Hi,
Thank you Troels for looking after this. As I didn't see any of
Karin's follow up emails, I assume that everything is now ok. Karin,
if there are still problems, please consider creating a bug report at:
https://gna.org/bugs/?func=additem&group=relax
There you'll be able to attach your files, scripts, etc. Note that
this will make any of your data public, so it is often a good idea to
truncate the files to 1 or 2 spin systems, and make sure that the
truncated file still trigger the problem you see.
Regards,
Edward
On 1 April 2016 at 01:45, Troels Emtekær Linnet <tlin...@nmr-relax.com> wrote:
> Dear Karin.
>
> Thank you for your last feedback.
>
> You are absolutely right.
> relax can indeed read NMRView type of files.
>
> My last comment on this was an error.
>
> I have produced a Tutorial page for you on the wiki:
> http://wiki.nmr-relax.com/Tutorial_for_R1/R2_Relaxation_curve-fitting_analysis_from_NMRView_files
>
> Under the point: Run analysis in relax GUI
> You can expand "the script" code by clicking "show" in the right side.
>
> These small snippets of codes is there to help reading "many" files.
> This is tedious work, when this is done manually.
>
> As I don't have all the files, I cannot test any further from this.
>
> Let me know how it goes. :)
>
> Best
> Troels
>
>
> 2016-03-31 22:35 GMT+02:00 Troels Emtekær Linnet <tlin...@nmr-relax.com>:
>
>> Hi Karin.
>>
>> Thank you for the file.
>>
>> The problem is, that relax currently does not recognize the file type of
>> NMRView.
>>
>> But the files contains all the information we need.
>>
>> We then have 2 options.
>>
>> 1) Either to make some custom scripts, that can convert the files to a
>> format that relax understands
>> 2) Or develop relax to understand NMRView files.
>>
>> My problem is, that I cannot find any documentation of the file type.
>> Can you help me with this?
>>
>> I am starting to writing down notes, so I can make a tutorial.
>>
>> ----
>>
>> This message can be found at:
>> http://thread.gmane.org/gmane.science.nmr.relax.user/1874
>>
>> Similar Tutorials for R1 can be found here:
>> http://wiki.nmr-relax.com/Main_Page
>> http://wiki.nmr-relax.com/Category:Tutorials
>>
>> http://wiki.nmr-relax.com/Tutorial_for_R1/R2_Relaxation_curve-fitting_analysis_on_varian_recorded_as_fid_interleaved
>>
>> This does not cover the current problem.
>> Relax cannot read NMRView *.xpk files.
>>
>> A similar problem can be seen here:
>>
>> http://wiki.nmr-relax.com/Tutorial_for_sorting_data_stored_as_numpy_to_on-resonance_R1rho_analysis
>>
>> We need to make modifications.
>> The whole list of files is:
>>
>> R1-methyl_hRGS4_20C_pH7_Mar2016_0ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_10msa
>> R1-methyl_hRGS4_20C_pH7_Mar2016_10msb
>> R1-methyl_hRGS4_20C_pH7_Mar2016_30ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_50ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_70ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_90msa
>> R1-methyl_hRGS4_20C_pH7_Mar2016_90msb
>> R1-methyl_hRGS4_20C_pH7_Mar2016_110ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_130ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_150ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_170ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_190ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_210ms
>> R1-methyl_hRGS4_20C_pH7_Mar2016_250ms
>>
>> Each file has a structure like this:
>>
>> ------------------------------------------------------------------------
>> label dataset sw sf
>> H1 C13
>> R1-methyl_hRGS4_20C_pH7_Mar2016_0ms.nv
>> 1500.2322998 3328.125
>> 599.802978516 150.824996948
>> H1.L H1.P H1.W H1.B H1.E H1.J H1.U C13.L C13.P C13.W C13.B C13.E C13.J
>> C13.U vol int stat comment flag0
>> 0 {75.HG11} 1.03960 0.03402 0.08416 ++ {0.0} {} {75.CG1} 21.00886 0.34258
>> 0.60154 ++ {0.0} {} 2.09171414375 0.0213 0 {} 0
>> 1 {75.HG21} 1.04055 0.03307 0.07450 ++ {0.0} {} {75.CG2} 20.65424 0.20240
>> 0.50941 ++ {0.0} {} 1.69693529606 0.0198 0 {} 0
>> ....
>> ------------------------------------------------------------------------
>>
>> This is 19 Columns of data.
>>
>> The first line describes what datatypes is to be found in the following
>> lines.
>> Here:
>> Line 1 is the label of nucleus
>> Line 2 is the dataset from where the file is created from
>> Line 3 is the Sweep (Spectral) Width [sw] in Hz
>> Line 4 is the Nuclear magnetic resonance frequency at the given
>> spectrometer field. In MHz.
>>
>> Then follow a line of header description.
>> H1.L must be the label for the H1. Residue 75, proton HG11
>> Then follows .P, .W and .B, which I don't know what it is?
>> The same for, .E, .J and .U.
>> Then comes for carbon C13.
>>
>> Ind the end, there must be the (vol) volume integration intensity and the
>> (int) the top point intensity?
>>
>> For determination of the errors of the intensity, I see that you have 2x
>> duplicated spectra (10ms, and 90ms.)
>> Is this what you wan't? Or do you want to measure the RMSD of the
>> background noise?
>> See:
>> http://wiki.nmr-relax.com/Spectrum_error_analysis
>> http://wiki.nmr-relax.com/RMSD
>>
>> Can you elaborate on:
>> .P, .W and .B
>> or .E, .J and .U. ???
>>
>> Best
>> Troels
>>
>>
>>
>>
>>
>> 2016-03-29 11:03 GMT+02:00 Troels Emtekær Linnet <tlin...@nmr-relax.com>:
>>
>>> Hi Karin.
>>>
>>> Can you provide the header or say 10 first lines of one of the files?
>>>
>>> Is the above the list of files used for the experiment?
>>>
>>> Best
>>> Troels
>>>
>>> 2016-03-25 0:47 GMT+01:00 Crowhurst, Karin A <karin.crowhu...@csun.edu>:
>>>
>>>> Hello,
>>>>
>>>>
>>>> I am new to Relax and have been trying to setup my R1 relaxation
>>>> analysis using the Relax GUI (4.0.1). My input files come from NMRView. I
>>>> opened all the files under "The file name(s)" menu - they all have .xpk
>>>> extensions (an example is R1-methyl_hRGS4_20C_pH7_Mar2016_0ms.xpk). I then
>>>> provided a set of spectrum ID string names that matched the filenames
>>>> (minus the .xpk extension - an example is
>>>> R1-methyl_hRGS4_20C_pH7_Mar2016_0ms). When I try to continue from that
>>>> window I get the following error:
>>>>
>>>>
>>>> RelaxError: Spectral data corresponding to the ID string
>>>> '['R1-methyl_hRGS4_20C_pH7_Mar2016_0ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_10msa',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_10msb',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_30ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_50ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_70ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_90msa',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_90msb',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_110ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_130ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_150ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_170ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_190ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_210ms',
>>>> 'R1-methyl_hRGS4_20C_pH7_Mar2016_250ms']' does not exist.
>>>>
>>>>
>>>>
>>>> Please help!
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Karin Crowhurst
>>>>
>>>> _______________________________________________
>>>> relax (http://www.nmr-relax.com)
>>>>
>>>> This is the relax-users mailing list
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>>>>
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>>>>
>>>
>>>
>>
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