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'
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