Dear all,
at first I would like to thank all of you for your fast responses! I
really appreciate your assistance and I am really thankful that there is
such a helpful and respectful NMR community out there!
I did not respond earlier to your previous messages, as I wanted to make
sure to not ran into another problem. I could figure out the reason for
the error of my previous described problem. The error with the 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
was caused by a question mark character in my peak list, which
originated in an unassigned nitrogen dimension of a residue in my CCPNMR
project:
Assignment w1 w2 Height
F142H-? 8.684 119.044 8.09E+04
So i could fix that problem by assign it and generate new peak lists for
my spectra and go on with the R1, R2 and NOE analysis without any
further issues. Then I tried to go on with a model free analysis. I
loaded the spins for protons and nitrogen from my previous described
sequence file and added the "element" attribute for each spin by hand.
When I tried to prepare the dipole-dipole interactions I came across
another error message which says:
relax>interatom.unit_vectors(ave=True)
Averaging all vectors.
RelaxError: Positional information could not be found for any spins.
I found an entry in the mailing list archive, where another user had
this issue
(https://www.mail-archive.com/[email protected]/msg01491.html). Is it
right, that I have to use a 3D structure instead of a sequence file for
the model free analysis, as only this will provide the necessary
positional information or did I do something wrong with loading my
sequence file?
Best regards and thanks for your help!
Hendrik
Am 16.02.22 um 23:55 schrieb Edward d'Auvergne:
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
--
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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