Re: Peak list reading -- December 21, 2013 - 02:42

Hi Min-Kyu.

I believe you probably need to define the right header

for the file.

ex:

      Assignment         w1         w2   Data Height

And see if you can fix the question marks.

568N-HN

Have a look in the test-suite for some typical definition of peaks files.

test_suite/shared_data/peak_lists

If you have a peak list, the new 3.1.1 version allow you to define the spins from 

a typical peak list.

spectrum.read_spins(file='peak_file.list', dir='/path/to/file')

Cheers

2013/12/20 Min-Kyu Cho <min-kyu.cho@xxxxxxxx>

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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