Difficulty with noe.py sample script -- October 06, 2008 - 15:37

Hello,

I am having trouble with the noe.py script. I have peptide data with 6 
backbone
15N labels, and I suspect it's a problem with input. I've tried several
permutations of full PDB file and full .list Sparky format files as well as
files trimmed down to include only the labeled residues. I'm not sure which is
preferable/required for input, and if unlabeled residues can simply be left
with a blank column value or if there is a special way to treat this?

Here is a sample of the output I get with any of my tries so far:

Scientific Python PDB parser.
Loading all structures from the PDB file.
Structure('select.pdb'):
  Peptide chain A of length 6


relax> structure.load_spins(spin_id='@N', ave_pos=True)
Adding the following spins to the relax data store.

Mol_name   Res_num    Res_name   Spin_num   Spin_name
A          254        LEU        68         N
A          258        LEU        142        N
A          261        GLY        197        N
A          264        LEU        230        N
A          268        ALA        294        N
A          273        LEU        366        N

relax> noe.read(file='NOnoe500_true.list', dir=None, spectrum_type='ref',
format='sparky', heteronuc='N', proton='HN', int_col=None)
Reference spectrum.
Traceback (most recent call last):
  File "/Applications/relax-1.3.1/relax", line 408, in <module>
    Relax()
  File "/Applications/relax-1.3.1/relax", line 125, in __init__
    self.interpreter.run(self.script_file)
  File "/Applications/relax-1.3.1/prompt/interpreter.py", line 270, in run
    return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag, 
show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
  File "/Applications/relax-1.3.1/prompt/interpreter.py", line 531, in
run_script
    return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
  File "/Applications/relax-1.3.1/prompt/interpreter.py", line 427, in
interact_script
    execfile(script_file, local)
  File "noe.py", line 36, in <module>
    noe.read(file='NOnoe500_true.list', spectrum_type='ref')
  File "/Applications/relax-1.3.1/prompt/noe.py", line 216, in read
    noe_obj.read(file=file, dir=dir, spectrum_type=spectrum_type, 
format=format,
heteronuc=heteronuc, proton=proton, int_col=int_col)
  File "/Applications/relax-1.3.1/specific_fns/noe.py", line 114, in read
    self.relax.generic.intensity.read(run=run, file=file, dir=dir,
format=format, heteronuc=heteronuc, proton=proton, int_col=int_col,
assign_func=self.assign_function)
AttributeError: Noe instance has no attribute 'relax'