NOE List Assignment

The Constraints Tools provide features for both analyzing and generating constraints for structure generation, and for assigning NOE spectra. The tool can take one or more peak lists and generate possible assignments for the peaks. A first step in the analysis displays the number of peaks that can be assigned, including a count of those with an excessive number of assignment possibilities. An iterative procedure can be used to automatically adjust the assignment tolerance to match a target fractional assignment.

Constraint Table

The constraint table displays a large amount of information about structural constraints. These constraints can be generated internally, through manual peak assignment, the peak identification tool, or the peak extract and assign mode of the constraint table. They can also be read in from external sources such as XPLOR constraint files, ARIA XML restraints files. The values displayed here were obtained upon reading in a merged STAR file from the BMRB containing assignments, constraints and a family of conformers.

Constraint Table Columns

Over 35 different values can be displayed for constraints. These include the atomic assignments, the origin peak, chemical shift violations, whether cross diagonal peaks were found, upper and lower distance constraints, and various distances both for the specific constraint, and averaged over all the constraints assigned to a peak. In addition there are columns for a network anchoring contribution, a distance violation contribution, and a summary value indicating the probability for the particular assignment. Bounds are graphically displayed within the table. The total amount of information can be somewhat overwhelming, so it is possible to turn on and off the display of each column.

Constraints by Residue

Filters can be set so that only constraints involving a single or pair of residues are displayed. This table is shown with a small set of columns, including the graphical bounds which illustrate the lower and upper bounds with triangles, the range of distances in the set of structures with a colored region, and the mean distance with a single vertical line. If bounds are violated the bound region is colored orange or red, depending on the violation.

Constraint Map

The residue-residue pattern of constraints is displayed in a map colored by the number of restraints between that residue pair. Clicking on an item in the map will filter the constraint table to show all constraints involving that pair of residues.

Restraint Map on Molecule

The Crescent Molecular viewer, a Java3D based viewer included with NMRViewJ Premium (support contract users) is integrated with the constraint table. If the viewer is active when a restraint map is created the restraints are displayed on the molecular structure.

Restraint Display on Molecule

If the molecular viewer is active then constraints for highlighted rows of the constraint table can be displayed on the molecular structure.

Dihedral Constraints

The dihedral constraint table shows any dihedral angle restraints. Triangles on the bounds display show the constraint values, and the shaded region shows the range of angles in the current set of structures. The table can generate all rows for all the phi, psi, and chi angles in the protein even if there are no constraints. This allows you to view the angle distribution in the existing structures.

News

2 August 2016: New Versions of NMRView, dataChord Spectrum Miner and Analyst, and NvFX

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Our first publication on NMRFx appears at the Journal of Biomolecular NMR