BMRZ Webportal
ARIA
ARIA Webportal

ARIA (Ambiguous Restraints for Iterative Assignment) is a software package by Michael Nilges for automated NOE assignment and NMR structure calculation. It uses an iterative structure calculation scheme and the final refinement in explicit water improves the quality of the calculated structures. More information and a manual about ARIA can be found on the ARIA website and on the ARIA discussion group on Yahoo. The ARIA software bundle, as implemented in this webportal is free for academic and educational purposes. The webportal is based on the ARIA version 1.2 package with several modifications (HJ development version).


Input files and parameters
Structure determination protocol for :
Number of structures per iteration (range 20-100) : Required! Invalid Format! Invalid Range! Invalid Range!
Number of structures in last cycle (range 20-200) : Required! Invalid Format! Invalid Range! Invalid Range!
Final number of refined structures (max 50) : Required! Invalid Format! Invalid Range! Invalid Range!
Seed (random number) for the calculation : Required! Invalid Format!


Sequence file (.seq) : Required!
Unambiguous distance restraints (.tbl) :
Ambiguous distance restraints (.tbl) :
Hydrogen bond restraints (.tbl) :
Dihedral angle restraints (.tbl) :
Planarity restraints (.tbl) :

NOESY peak lists
The NOESY peak lists and resonance lists can either be in Sparky (.list), Xeasy (.peaks and .prot), NMRView (.xpk) or Ansig (.crp) format. Select for all peak lists the format (columns) and the chemical shift tolerances (ppmd) for assignment of each nucleus. The values for the NOESY mixing time, rotation correlation time and spectrometer frequency are only required when using correction of spin diffusion. Take care of the right atom nomenclature (eg. such as HN for the protein amides and H5'1 and H5'2 for nucleotide backbone protons). The Xeasy setup uses the IUPAC convention (eg. HB2 and HB3 instead of HB1 and HB2) and all the others use the standard ARIA/CNS forcefield nomenclature (eg. for protein: allhdg5.3 and for nucleic acid: dna-rna-allatom-hj)

Peak list format :
Enable floating chirality assignment (swapping)


Peak list 1 :       
Resonances :        Reset bounds of systematic violations
Proton 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Correct for spin diffusion and exchange
Hetero 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        NOESY mixing time (ms) : Invalid Format! Invalid Range! Invalid Range!
Proton 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Rotation correlation time (ns) : Invalid Format! Invalid Range! Invalid Range!
Hetero 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Spectrometer frequency (MHz) : Invalid Format! Invalid Range! Invalid Range!


Peak list 2 :       
Resonances :        Reset bounds of systematic violations
Proton 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Correct for spin diffusion and exchange
Hetero 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        NOESY mixing time (ms) : Invalid Format! Invalid Range! Invalid Range!
Proton 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Rotation correlation time (ns) : Invalid Format! Invalid Range! Invalid Range!
Hetero 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Spectrometer frequency (MHz) : Invalid Format! Invalid Range! Invalid Range!


Peak list 3 :       
Resonances :        Reset bounds of systematic violations
Proton 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Correct for spin diffusion and exchange
Hetero 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        NOESY mixing time (ms) : Invalid Format! Invalid Range! Invalid Range!
Proton 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Rotation correlation time (ns) : Invalid Format! Invalid Range! Invalid Range!
Hetero 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Spectrometer frequency (MHz) : Invalid Format! Invalid Range! Invalid Range!


Peak list 4 :       
Resonances :        Reset bounds of systematic violations
Proton 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Correct for spin diffusion and exchange
Hetero 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        NOESY mixing time (ms) : Invalid Format! Invalid Range! Invalid Range!
Proton 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Rotation correlation time (ns) : Invalid Format! Invalid Range! Invalid Range!
Hetero 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Spectrometer frequency (MHz) : Invalid Format! Invalid Range! Invalid Range!


Peak list 5 :       
Resonances :        Reset bounds of systematic violations
Proton 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Correct for spin diffusion and exchange
Hetero 1 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        NOESY mixing time (ms) : Invalid Format! Invalid Range! Invalid Range!
Proton 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Rotation correlation time (ns) : Invalid Format! Invalid Range! Invalid Range!
Hetero 2 :    Tolerance (ppm) :   Invalid Format! Invalid Range! Invalid Range!        Spectrometer frequency (MHz) : Invalid Format! Invalid Range! Invalid Range!

Residual Dipolar Couplings
RDCs can be used in the form of SANI (susceptability anisotropy) type restraints in the standard ARIA/CNS format. The residue number of the alignment tensor is 999. Define the proper parameters for the tensor and take care of the nuclei scaling factors (eg. from PALES: R=Dr/Da and A=Da*DI, in which DI is about 21700 for the protein amide).

Residual dipolar coupling restraint file (.tbl) :
First iteration in which RDCs will be used (range 0-8) : Invalid Format! Invalid Range! Invalid Range!
Rhombicity coefficient (R) of the alignment tensor : Invalid Format! Invalid Range! Invalid Range!
Axial coefficient (A) of the alignment tensor : Invalid Format! Invalid Range! Invalid Range!

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