On Wed, 16 Feb 2022 at 19:25, Hendrik Kirschner via nmr-relax-users
<[email protected]> wrote:
>
> Dear all,
>
> I am new to Relax and wanted to analyze my relaxation data with it. I used
> CCPNMR V2.4.2 to export my peak lists from my T1, T2 and NOE data sets in
> sparky format. Also the sequence file was generated with CCPNMR V2.4.2. Then
> i started the analysis with relax 5.0.0 at NMRbox.org. The loading of the
> spins from the sequence file was successfull and spin container for all
> residues were generated with H and N spins in it each.
>
> My sequence file is formatted like this:
>
> res_num res_name spin_num spin_name
> -2 Gly -2 N
> -1 His -1 N
> 0 Met 0 N
> 1 Ser 1 N
>
> But when i tried to load my relaxation data ("peak intensity reading" window)
> i always get the following error message:
>
> relax>
> spectrum.read_intensities(file='/home/nmrbox/0001/hkirschner/Desktop/Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms',
> dir=None, spectrum_id='5', dim=1, int_method='height', int_col=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, ncproc=None)
> Opening the file
> '/home/nmrbox/0001/hkirschner/Desktop/Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms'
> for reading.
> Sparky formatted data file.
>
> Number of header lines found: 1
> 2D peak list detected.
>
> Traceback (most recent call last):
> File "/usr/software/relax/gui/interpreter.py", line 109, in apply
> fn(*args, **kwds)
> File "/usr/software/relax/pipe_control/spectrum.py", line 610, in read
> peak_list = read_peak_list(file=file[file_index], dir=dir,
> int_col=int_col, spin_id_col=spin_id_col, mol_name_col=mol_name_col,
> res_num_col=res_num_col, res_name_col=res_name_col,
> spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
> spin_id=spin_id)
> File "/usr/software/relax/lib/spectrum/peak_list.py", line 213, in
> read_peak_list
> sparky.read_list(peak_list=peak_list, file_data=file_data)
> File "/usr/software/relax/lib/spectrum/sparky.py", line 127, in read_list
> name2 = row2[-2] + row2[-1]
> IndexError: list index out of range
>
> The sparky format of the data looks like this:
>
> Assignment w1 w2 Height
> K18H-K18N 8.134 123.117 6.63E+05
>
>
> I tried different settings in the "peak intensity reading" window (e.g.
> intensity column set to 3 or 4). I also searched in the mailing list and Wiki
> for a solution and found an entry which seems to describe my problem (-> bug
> #22961; found at: http://wiki.nmr-relax.com/Relax_release_bugfixes), but the
> description does not really helped me. I also tried a different Relax version
> (V4.1.3) and to load the spins via a PDB-file, but it leads to the same error.
>
> Is there anything wrong with my formats or did I do something wrong in the
> settings?
Hi Hendrik,
Welcome to the relax mailing lists! That is an interesting problem
that I don't think anyone has encountered before. I wonder if it is
due to CCPN not producing a conformant Sparky formatted file. For the
example you gave, I can see that the 'K18H-K18N' assignment works ok.
Using the python3 interpreter and replicating the failing lines of
code:
>>> from re import split
>>> assign2 = "K18N"
>>> row2 = split('([a-zA-Z]+)', assign2)
>>> row2[-2] + row2[-1]
'N'
relax correctly finds 'N' for the name of the 2nd dimension. What you
could do is to randomly delete blocks of lines from your
Apo_Dynamik_Auswertung/T1_600er_sparky/T1_600_5ms file, running relax
to find which line is causing the error. You should be able to repeat
this until you only have a single failing line left. If you could
find that line and report it back, that would be appreciated. I can
then see if it is something that should be fixed in relax or in the
CCPN Sparky export.
Cheers,
Edward
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