I ran the 1.2 version of the noe.py script with the 1.2 version of
relax on the
same machine and had a slightly different error output (below). If this is
simply a version-change problem with the script as you say, then I'm not sure
why I'd get a convoluted error with version 1.2 as well.
Output:
Calculating and averaging the unit XH vectors from all structures.
relax> noe.read(run='noe', file='NOnoe500.list', dir=None,
spectrum_type='ref',
format='sparky', heteronuc='N', proton='HN', int_col=None)
Reference spectrum.
Sparky formatted data file.
Opening the file 'NOnoe500.list' for reading.
Number of header lines found: 2
Traceback (most recent call last):
File "/Applications/relax-1.2.14/relax", line 457, in <module>
Relax()
File "/Applications/relax-1.2.14/relax", line 167, in __init__
self.interpreter.run()
File "/Applications/relax-1.2.14/prompt/interpreter.py", line 216, in run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File "/Applications/relax-1.2.14/prompt/interpreter.py", line 391, in
run_script
console.interact(intro, local, script_file, quit)
File "/Applications/relax-1.2.14/prompt/interpreter.py", line 343, in
interact_script
execfile(script_file, local)
File "noe_12.py", line 35, in <module>
noe.read(name, file='NOnoe500.list', spectrum_type='ref')
File "/Applications/relax-1.2.14/prompt/noe.py", line 226, in read
self.__relax__.specific.noe.read(run=run, file=file, dir=dir,
spectrum_type=spectrum_type, format=format, heteronuc=heteronuc,
proton=proton,
int_col=int_col)
File "/Applications/relax-1.2.14/specific_fns/noe.py", line 110, 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)
File "/Applications/relax-1.2.14/generic_fns/intensity.py", line 232, in read
res_num, H_name, X_name, intensity = self.intensity(self.file_data[i])
File "/Applications/relax-1.2.14/generic_fns/intensity.py", line 92, in
intensity_sparky
intensity = float(line[self.int_col])
IndexError: list index out of range
Quoting Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>:
Hi,
This is definitely a bug! If you could file a bug report
(https://gna.org/bugs/?func=additem&group=relax), that would be much
appreciated. If you would like a description of how this is done,
please see section 3.3 of the relax manual (version 1.3) or the online
HTML version (currently at
http://www.nmr-relax.com/manual/1.3/node49.html).
The reason this is failing is because this code in the 1.3 relax
versions has not been converted to the new design yet. For me or the
relax developers to implement this, first a system test should be
added to the test suite. The test suite can be run by typing:
$ relax --test-suite
The system test is simply a very tiny, although complete, version of
the analysis you would like to do. This can include a small subset of
the base data, randomised if you'd like to protect the data prior to
publication. With the small data subset, I can include your full
analysis script into the test suite and execute it with the data.
Then once the test passes, an NOE analysis will be possible. The data
and script can be attached to the bug report. If you would like to
help in getting this test implemented, that would be much appreciated.
Thanks,
Edward
On Mon, Oct 6, 2008 at 3:31 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
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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Re: Difficulty with noe.py sample script