Dear Hendrik,
I have not used Relax for T1/T2/NOE data (I assume you are planning to
do model-free analysis). However, for CPMG analysis I have the following
formats for my input files:
_Peak intensity files:_
Assignment w1 w2 Data Height
ASP2N-HN 8.560 122.651 2.98553e+08
SER3N-HN 8.425 116.521 2.47809e+08
THR4N-HN 8.358 115.634 2.42621e+08
SER5N-HN 8.264 117.706 2.65439e+08
_Sequence file (no headers):_
2 Asp
3 Ser
4 Thr
5 Ser
In the relax script this is loaded as:
# Load the sequence.
sequence.read('sequence.txt', dir=DATA_PATH, res_num_col=1, res_name_col=2)
I hope this helps. The sequence file format seems to be quite different.
The variable number of spaces between your first and second columns may
cause problems.
Best wishes,
Mark
On 16/02/2022 18:25, Hendrik Kirschner via nmr-relax-users 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?
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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