Discussion group for the ARIA software

[Benjamin Bardiaux <bardiaux AT pasteur.fr>]

Hi,

It could also come from incorrect dimension mapping at the conversion stage. Please check that Proton1/Hetero1 and 
Proton2/Hetero2 in the conversion XML point to the right columns in the original peak-list.

Best,

Benjamin


On 07/09/2022 13:08, Christoph Wiedemann wrote:
> Hello Raoul,
>
> I had the same error message before. The reason was that there was a mismatch 
> between the chemical shifts in the peak lists and the chemical shifts in the 
> assignment list. After re-referencing the spectra and peak lists, the 
> structure calculation went through correctly.
>
> With best regards,
> Christoph
>
> > Am 07.09.2022 um 07:35 schrieb rvaz AT uoguelph.ca:
> >
> > Hello,
> >
> > I am attempting to perform a structure calculation using ARIA through NMRbox.
> > I've managed to reach the stage where assignments of unambiguous peaks begins,
> > but seem to run into an error which I've included.
> >
> > I had initially thought this was a problem with my data or input files, and so
> > attempted to use data provided on the ARIA website
> > (http://aria.pasteur.fr/documentation/tutorials/spin-diffusion-correction) as
> > a test. However, this results in the same error, which leads me to believe it
> > may be something else.  had attempted increasing the frequency windows, as
> > well as verifying all dimensions were consistent, but to no avail.
> >
> > I am able to have the calculation run successfully to completion using my data
> > which contains only unambiguous distance/angle/h-bond restraints in the .tbl
> > format. However, it seems that as soon as I attempt to include spectra in the
> > form of assignments and a list of ambiguous peaks, it results in the error
> > above. I
> >
> > Any suggestions or help would be appreciated, and thank you.
> >
> > Raoul Vaz
> > Protein NMR Research Group
> > University of Guelph
> > Guelph, ON Canada
> >
> >
> > MESSAGE [Project]: -------------------- Reading data --------------------
> > MESSAGE [Project]: Cache is enabled.
> > MESSAGE [Project]: Cache file does not exist. Creating new file.
> > MESSAGE [Project]: Reading molecule definition /home/nmrbox/0012/rvaz/Desktop/
> >                    nilges/rad/run1/data/sequence/tudorseq.xml.
> > MESSAGE [Project]: Reading spectrum /home/nmrbox/0012/rvaz/Desktop/nilges/rad/
> >                    run1/data/spectra/15Nnoesy_peaks.xml.
> > MESSAGE [Project]: Reading chemical shift list /home/nmrbox/0012/rvaz/Desktop/
> >                    nilges/rad/run1/data/spectra/15Nnoesy_prot.xml.
> > MESSAGE [Project]: Data files read.
> > MESSAGE [Project]: Data files cached.
> > MESSAGE [Project]: ------------------- Filtering input data
> > -------------------
> > MESSAGE [Project]: Applying filters to spectrum/shiftlist "15Nnoesy":
> > MESSAGE [Project]: Chemical shift list filtered: 452 / 604 shifts (74.83 %)
> >                    removed.
> > MESSAGE [Project]: NOESY spectrum "15Nnoesy" filtered: 0 / 495 peaks (0.00 %)
> >                    removed. Details:
> > MESSAGE [Project]: - no. of invalid proton 1 shifts: 0
> > MESSAGE [Project]: - no. of invalid proton 2 shifts: 0
> > MESSAGE [Project]: - no. of invalid peak sizes:      0
> > MESSAGE [Project]: - no. of diagonal peaks:          0
> > MESSAGE [Project]: - no. of unassigned peaks:        0
> > MESSAGE [NOESYSpectrumFilter.TP]: Spectrum filter report written to file "/
> > home/
> >                                   nmrbox/0012/rvaz/Desktop/nilges/rad/run1/
> > data/
> >                                   spectra/peak_list.filtered"
> > MESSAGE [Project]: ---------------- Preparing structure engine
> > ----------------
> > MESSAGE [CNS]: Sequence PDB-file written.
> > MESSAGE [CNS]: CNS output file has been copied to "/home/nmrbox/0012/rvaz/
> >                Desktop/nilges/rad/run1/cns/begin/generate.out".
> > MESSAGE [CNS]: PSF-file has been created.
> > MESSAGE [CNS]: CNS output file has been copied to /home/nmrbox/0012/rvaz/
> >                Desktop/nilges/rad/run1/cns/begin/generate_template.out.
> > MESSAGE [CNS]: Template PDB-file has been created.
> > MESSAGE [Project]: Starting ARIA main protocol on Tue Sep  6 22:46:15 2022
> > MESSAGE [Project]: -------------------- Assigning spectra --------------------
> > MESSAGE [Project]: Creating seed assignment for spectrum "15Nnoesy" ...
> > WARNING [Project]: More than 90% of the cross peaks could not be assigned.
> > This
> >                    might be due to interchanged frequency dimensions or
> >                    undersized frequency windows. Please check your setup.
> >
> > ARIA halted at Tue Sep  6 22:46:15 2022.


--
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Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
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