Discussion group for the ARIA software

["Higman, Vicky (Dr.)" <vad5 AT leicester.ac.uk>]

Hi Raoul,

 

I wonder if this is what I encountered once: when using the Spin Diffusion Correction, it can sometimes end up giving you negative distances or something like that. Have a look at the restraint files generated. The answer was to switch off the spin diffusion correction for the first few iterations.

Hope that helps.

 

Best wishes,

Vicky

 

 

From: aria-discuss-request AT services.cnrs.fr <aria-discuss-request AT services.cnrs.fr> on behalf of rvaz AT uoguelph.ca <rvaz AT uoguelph.ca>
Date: Wednesday, 7 September 2022 at 06:24
To: aria-discuss AT services.cnrs.fr <aria-discuss AT services.cnrs.fr>
Subject: [aria-discuss] ARIA error - cross peak assignment

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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
(https://eur03.safelinks.protection.outlook.com/?url="http%3A%2F%2Faria.pasteur.fr%2Fdocumentation%2Ftutorials%2Fspin-diffusion-correction&amp;data=05%7C01%7Cvad5%40leicester.ac.uk%7C0d0def6d0dba49f74b6f08da90914a47%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637981250944604145%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=cw0%2Bx2gseQNB7Ld1MyuhyNOqp916joMD7ydW5wrWyrI%3D&amp;reserved=0) 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.