NMR Vivaldi

pdbe.org/vivaldi

Vivaldi: Visualisation, analysis and validation of NMR entries
Home | Wizard | Manual  
 

Welcome to the Vivaldi wizard


Enter a PDB entry code below to check the availability of each visualisation.


Submit

Cluster visualisation

Whenever multiple models are deposited for an NMR entry, the PDBe OLDERADO service groups similar models into clusters and identifies core domains of the protein. The NMR viewer can either be used to visualise the similarities and differences between or within clusters or to visualise the core domains.

Do you wish to visualise protein domains as calculated by NMRCore?

  • Show domains on most representative model
  • Show domains on one model for each cluster
  • Show domains on every model

Do you wish to visualise differences/similarities between or within clusters as calculated by NMRClust?

  • Show one model for each cluster
  • Show all models
  • Show all models of the main cluster

Display in viewer Back

Experimental data visualisation

Models deposited for an NMR entry can be validated using experimental data provided within the deposition such as chemical shifts and/or distance constraints. The Validation of Archived chemical Shifts through atomic COordinates (VASCO) service is used to compare the deposited chemical shifts to those of atoms in different proteins but similar environments. A Z-score providing a measure for the "normality" of chemical shifts can be visualised in the NMR viewer.
Constraints are grouped per residue and per type (intra-residue, ...) and can be visualised on any model. Violations are shown coloured by the severity of the violation.

Show dihedral constraints

  • All constraints

Show dihedral constraint violations

  • All violations

Display in viewer Back

Show distance constraints

  • All constraints
  • Intra-residue constraints
  • Short range constraints
  • Medium range constraints
  • Long range constraints

Show distance constraint violations

  • All violations
  • Intra-residue violations
  • Short range violations
  • Medium range violations
  • Long range violations

Display in viewer Back

Show RDC constraints

  • Scatter plot showing experimental and fitted couplings
  • Plot showing differences between experimental and fitted couplings

Display in viewer Back

Show chemical shift outliers

  • For all atom types
  • For hydrogen atoms only
  • For carbon atoms only
  • For nitrogen atoms only

Display in viewer Back

Validation score visualisation

Models deposited for an NMR entry can be validated using general knowledge of protein structure. The NMR viewer uses per residue CING, WHAT IF and PROCHECK scores to validate the deposited models.

CING "red-orange-green" score

  • This score is basically an overall score per residue taking into account all the following WHAT IF and PROCHECK scores as well as constraint violations. Residues are coloured green if all tests are passed, orange if minor issues are observed and red if major issues are observed.

WHAT IF Scores

  • WHAT IF Ramachandran: Z-score for you, which can tell you whether or not the Ramachandran plot "looks OK"
  • WHAT IF Bonds: the RMS deviation from the mean Engh and Huber parameters, expected to be around 1.0.
  • WHAT IF Angles: Z-score for all angles
  • WHAT IF Backbone: Z-score of 5 C-alpha coordinates in WHAT IF database
  • WHAT IF Unusual short contacts: prints the amount by which VdW contacts are too short
  • WHAT IF Chi1 - Chi2: Z-score will be calculated that expresses how normal the Chi-1 and Chi-2 angles in this structure are
  • WHAT IF Peptide plane: verifies that the variation in Omega angles observed in the protein is "normal"
  • WHAT IF Inside - Outside: Z-score for expected solvent accessibility
  • WHAT IF Sidechain Planarity: planarity of sidechains of protein residues is verified against a database distribution
  • WHAT IF Rotamers: compare the Chi-1 rotamer of all residues with the distribution of observed rotamers for the same residue type in a similar local backbone conformation in the database
There is a complete description of the output of all WHAT IF checks here.

PROCHECK Scores

  • PROCHECK Overall: log-odds score
  • PROCHECK Ramachandran: log-odds score for Phi and Psi angles
  • PROCHECK Chi1 - Chi2: log-odds score for sidechain angles
  • PROCHECK Chi1: log-odds score for Chi1 sidechain angle

Display in viewer Back