Check for assignment errors

Instructions

In order to check your peaks or assignments for possible errors, conflicts or other problems, you can use the M: Assignment: Quality Reports.

The {Atom Assign Status} tab in the Assignment: Quality Reports popup gives assignment percentages for each atom type and residue type. This information shows how complete your assignments are and keeps track of what is still left to assign.

The {Resonances} tab (shown below) shows the resonances under |Resonance|, their shifts under |Value|, and various kinds of statistics:

• • |SD| is the standard deviation over the observed shifts

  • |Max Peak Delta Δ| is the difference between the largest and smallest shift value.

  • |Contribs| is the number of contributions to the assignment

Fields that show improbable values are colored red, showing that they need a second look (even if they still may be correct). For each row |Resonance| shows the assignment and |Bound| shows other atoms that are set to be covalently bound to the resonance through assignments that were made. Both |Resonance| and |Bound| may show assignment errors, duplicated assignments, etc.. To inspect an assignment, select the row and click [Show Peaks] or [Show Resonances] to display data. For example, you can sort on |Max Peak Δ| to discover resonances that have a small standard deviation, but a large maximum deviation. This suggests that at least one peak is out of line. Lots of red warnings in the {Resonances} tab, especially in the |Bound| column, may indicate a problem with the specification of one or more experiment types, rather than a direct problem with the peak assignments.

The {Peaks} tab lists the peaks. Various kinds of statistics are found under |Volume|, |Height|, |Log Vol Dev| and |Log Height Dev|. |Log Vol Dev| and |Log Height Dev| stand for the standard deviations of the peak integration volume or peak height on a logarithmic scale. These measures highlight therefore peaks that are outliers in terms of their volume or intensity (strong/weak).  Pink colored cells indicates potential alerts and red colored cells indicates alerts. Much of how to interpret things will depend on the experiment type. For example a really weak NOE peak may be acceptable, but a really weak HNCO may not.