Discussion group for the ARIA software

[Christoph Wiedemann <christoph.wiedemann AT biochemtech.uni-halle.de>]

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.
> 
>