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?
Best regards,
Hendrik
--
Hendrik Kirschner, M.Sc.
Biomolecular NMR (NC5/173 Süd)
Faculty of Chemistry and Biochemistry
Ruhr-University Bochum
Universitaetsstrasse 150
44801 Bochum
Germany
[email protected]
Tel.: +49 234 32-26246
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