Hi,
Sorry about the delay in responding, I've been on holidays until
today. You are correct about noe.read() being removed from the
repository. This has been replaced by spectrum.read_intensities().
You can see which user functions are now necessary to set up a
steady-state NOE analysis by looking at the sample_scripts/noe.py
script. Looking at the new code in generic_fns.spectrum.read(), I can
see that the function checks for the presence of sequence data in the
relax data store before printing out the peak list file type. So the
problem described by Ryan no longer exists in relax as noe.read() has
been deleted and replaced. Therefore I'll close the bug report.
Cheers,
Edward
On Thu, Dec 18, 2008 at 4:41 AM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:
Hi all,
I just checked the code and it seems that relax already throws an error
before doing anything when no sequence is present (see lines 739-740 in
generic_fns/spectrum.py)... Indeed, when trying to load a file directly,
the sequence error is thrown first :
relax> pipe.create('NOE', 'noe')
relax>
spectrum.read_intensities(file='test_suite/shared_data/peak_lists/ref_ave.list',
spectrum_id='any')
RelaxError: The sequence data does not exist.
But maybe this is related to the noe.read() function, as written in the
previous posts. Ed, could you help me in figuring out what happened to
this function in the repository ? It seems to have disappeared... Is it
replaced by the spectrum.read_intensities() function I used above ? If
yes, and if the bug is absent from the repository, can we think of it as
fixed ?
Regards,
Séb :)
Edward d'Auvergne wrote:
Seb, I would treat this one as a bug. We need to get the test for the
existence of a loaded sequence before the print out of 'Reference
spectrum' and 'Sparky formatted data file' to avoid confusion. Ryan,
the issue here is not the reading of the file but the fact that relax
requires a sequence of spins to be loaded prior to doing anything, be
that backbone N spins for a protein, all C spins in a small molecule
or a set of specific N and C spins per residue in RNA. This can be
done using sequence.read() or structure.read_pdb() followed by
structure.load_spins().
Regards,
Edward
On Tue, Dec 16, 2008 at 8:25 PM, Ryan MB Hoffman
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
Follow-up Comment #8, bug #11913 (project relax):
When I change the noe.read line to:
noe.read(file='test.list',spectrum_type='ref',format='sparky')
the output reads:
Reference spectrum.
Sparky formatted data file.
RelaxError: The sequence data does not exist.
So it looks like the data is read successfully (although I have more
inputs
to test) but I need to have the protein sequence defined, correct?
Also, I suggest changing the docstring for noe.read from "sequence data"
to
"relaxation data." That's a typo I've caught, right?
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Re: [bug #11913] Problems with reading Sparky formatted file