Re: Difficulty with noe.py sample script -- October 07, 2008 - 16:44

Hi,

This is again a bug, as relax hasn't managed to catch a file formatted
in a way it cannot recognise and then respond with a error message
which is understandable.  The error indicates to me that relax is
thinking this is a Sparky formatted peak list, but that the intensity
column is missing (at least in one position).  The file should look
something like:

      Assignment         w1         w2   Data Height

         LEU3N-HN    122.454      8.397       129722
         GLY4N-HN    111.999      8.719       422375
         SER5N-HN    115.085      8.176       384180
         MET6N-HN    120.934      8.812       272100
         ASP7N-HN    122.394      8.750       174970
         SER8N-HN    113.916      7.836       218762
        GLU11N-HN    122.194      8.604        30412
        GLY12N-HN    110.525      9.028        90144

The NOE analysis works in version 1.2.14, but not in 1.3.1 yet.  The
idea for filing the bug report and then me creating a system test
within relax using a tiny subset of the data was simply a suggestion
that would allow me to quickly make the NOE analysis functional in the
next relax 1.3 version.  Then other relax users would benefit from
having this code functional again too.  But if you need the NOE data
quickly, relax 1.2.14 will do the job with a Sparky peak list
possessing all four columns.

Regards,

Edward



On Tue, Oct 7, 2008 at 4:12 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> 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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