Analyse restraints and violations for a generated structure

Introduction

The Structure: Restraints and Violations popup (M: Structure: Restraints and Violations) in Analysis is used for management and display of restraints and violations. Restraints are listed in restraint lists and are found in the {Restraints} tab. Violations are listed in violation lists and are found in the {Violations} tab. How the analysis of restraints and violations in Analysis is done in practice tends to vary with personal preference and this HowTo is merely made to illustrate some of the functionalities.

Restraints

Before a violation analysis has been performed, restraints are listed as green and grey rows in the {Restraints} tab. The green rows mark the start of a restraint set. The grey rows represent alternative contributions of restrained resonances (e.g. a different pair of atoms), in the same restraint set. The green and grey rows have in common the same (restraint) |Value|:

At the bottom of the table there is the [Delete Items] button to remove restraints. Both the restraint and the alternatives that have the same |Value| will be deleted, even if only one of them was selected. To delete a restraint alternative, select it and click [Delete Items]. The other various functions below the table also allow restraints to be managed. Several functions are used to link restraints and peaks:

• • Select one or several restraint(s) and click [Show Peaks]. This will open the Peak: Selected Peaks popup that contain the peak(s) that gave rise to the restraint(s). Note that a restraint may be linked to more than one peak, for example where there are symmetry related peaks that correspond to the same close resonance pair. In the Peak: Selected Peaks popup, select e.g. a peak and click [Find Peak] to display the peak in the associated spectrum.

  • Select a restraint and click [Assign Peak] to open the Assignment: Assignment Panel popup, which shows assignment possibilities and status for the peak that gave rise to this restraint.

  • Select a peak in a spectrum and click [Show Restraints for Selected Peaks] to highlight the associated restraint in the restraints table.

  • Click [Update Peak Assignments] to refresh peaks according to restraints (e.g. after an ARIA or CYANA run that removes restraint ambiguity)

  • Click [Update Assignment From Peak] to refresh restraints according to peak assignments.

For distance restraints:

• • Set method for calculate distances in the “Value Method:” pulldown menu. The “Minimum” method simply records the shortest distance between any pair of atoms from either side of the restraint (e.g. the closes atoms in two methyls). The “NOE sum” method uses r^-6 distance summation to give a value that represents what the equivalent NOE estimated distance would be if a signal were recorded between two atom groups.

Structures and Violations

Select a structure from the “Structure:” pulldown menu to allow geometric information to be extracted from the structure ensemble in the |Struc Value| column. Those values can be compared with the values that are being restrained.

• • Set “Violation List:” to “<New>“ and click [Calculate Violations] to perform a structure violation analysis, which stores the violations in a new violation list. The [Calculate Violations] function will not work until a structure is selected. Any restraints that were violated in a structural analysis will be coloured; red, orange or yellow depending on severity. The average violation over a structure ensemble are recorded in the |Mean Viol| column. The proportion of an ensemble’s models that were violated are recorded in the |Viol Fraction| column.

The table in the {Violations} tab presents some of the same information as the table in {Restraints}. The data is merely presented in a different way. Note that a violation list can store violations coupled to different kind of restraints. Select a violation in the table and click:

• • [Show Restraint], to view the restraint that was violated in the {Restraints} tab.

  • [Assign Peak], to go to the Assignment: Assignment Panel popup for the peak that is associated with the violated restraint.

  • [Show Peaks], to display the peak that gave rise to the restraint (via the Peak: Selected Peaks popup).

More about how to analyse restraints and violations

See the Calculating structural violations section in Basic tutorial and the Restraints & Violations section in the Protein structure calculation tutorial.