Hi ,
I got sparky peak list file written as
568?-? 123.445 8.765 3.45E06
. . . . .
When I tried to read in this file through GUI, it complains
----------
Sparky formatted data file.
Number of header lines found: 1
2D peak list detected.
RelaxWarning: Improperly formatted Sparky file, cannot process the residue
name for dimension 1 in assignment: 546N-H. Setting residue name to None.
RelaxWarning: Improperly formatted NMRPipe SeriesTab file, cannot process
the residue name for dimension 2 in assignment: 546N-H. Setting residue name
to None.
Traceback (most recent call last):
File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/wizards/wiz_objects.py",
line 161, in _apply
self.exec_status = self.on_execute()
File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/uf_objects.py", line 883,
in on_execute
return_status = self.execute(self.name, **kargs)
File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/uf_objects.py", line 805,
in execute
return_status = interpreter.apply(uf, *args, **kwds)
File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/interpreter.py", line 109,
in apply
apply(fn, args, kwds)
File "/home/mkc9/Programs/RELAX/relax-3.1.1/pipe_control/spectrum.py",
line 530, in read
peak_list = read_peak_list(file=file, 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 "/home/mkc9/Programs/RELAX/relax-3.1.1/lib/spectrum/peak_list.py",
line 208, in read_peak_list
sparky.read_list(peak_list=peak_list, file_data=file_data)
File "/home/mkc9/Programs/RELAX/relax-3.1.1/lib/spectrum/sparky.py", line
203, in read_list
intensity = float(line[int_col])
IndexError: list index out of range
-----
Since I already made sequence & spin system with correct residue number, I
expected the residue number in Sparky file should be enough.
So,my questions are:
1. the sparky file format for relax should be made as written in the manual?
2. Can relax recognize FASTA sequence and automatically generate Spin
system?
Thanks and Happy Holiday!
Min-Kyu
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