This popup provides statistics and quality reports on several data types in the project. It allows the user to easily identify potential inconsistencies, errors or unusual values, and provides direct access to the peaks and their properties that may give rise to the identified problems.

Atom Assign Status

The {Atom Assign Status} tab gives a statistical overview of the chemical shift assignments for a selected molecular chain and chemical shift list in the project. 

The Assignment: Quality Reports popup (Atom Assign Status).

Mol System

Specifies the molecular system for which to display the atom assignment statistics.

Shift List

Specifies the chemical shift list for which to display the atom assignment statistics.

Atom Assign Status table

This table lists all the atom assignment statistics grouped into a variety of categories for the selected molecular chain and chemical shift list.

Category

The category for which statistics are given. Category names are self-explanatory, and can be based on:

• • Element

  • Amide

  • Backbone

  • Side Chain

  • Type

  • Residue

  • etcetera

Available

The number of possible assignments in the category.

Assigned

The number of assignments in the category.

% Assigned

The percentage of assignments made in the category.

Min Shift

The minimum chemical shift in the category.

Mean Shift

The mean chemical shift in the category.

Max Shift

The maximum chemical shift in the category.

Through-Space Status

The {Through Space Status} tab gives a statistical overview of the assignments of through space connections for a selected molecular system and peak list in the project. Peaks that are connected to a selected residue can be shown in the Peaks: Selected Peaks popup using the [Show Peaks] button.

The Assignment: Quality Reports popup (Through Space Status).

Mol System

Specifies the molecular system for which to display the statistics of the through-space connectivities.

Peak List

Specifies the peak list for which to display the statistics of the through-space connectivities.

Through-Space Status table

This table lists the statistics of the through-space connectivities for the selected molecular chain and chemical shift list. The table includes overall numbers for each Chain, followed by the individual numbers for each residue in that chain.

Residue

The residue number and Ccp Code for the residue, or the Chain identifier.

Total

The total number of through-space connectivities.

Intra Residue

The total number of intra residue through-space connectivities.

Inter Residue

The total number of inter residue through-space connectivities.

Sequential

The total number of sequential (i, i+1) through-space connectivities.

Short Range

The total number of short range (i, i+2) through-space connectivities.

Short Non-seq

The total number of short range non sequential through-space connectivities.

Long Range

The total number of short range (i, >i+5) through-space connectivities.

Intra Chain

The total number of through-space connectivities found within the molecular chain.

Inter Chain

The total number of through-space connectivities found from the current molecular chain to another molecular chain.

Contacted Residues

The residue numbers of the contacted residues.

Resonances

The {Resonances} tab gives a list of all the resonances and a quality assessment thereof using the selected chemical shift list. Statistics of the chemical shifts of the resonances are displayed, checked internally and compared to reference databases. Abnormalities in the chemical shifts, such as unusual values or high standard deviations are highlighted in red for very abnormal values or in yellow-green for unlikely values. The highlighting allows the user to quickly assess any problems. Peaks that are connected to a selected resonance can be shown in the Peaks: Selected Peaks popup using the [Show Peaks] button.

The Assignment: Quality Reports popup (Resonances).

Shift List

Specifies the chemical shift list that is used for the quality assessment.

Resonances table

This table lists all the resonances with their properties.

#

The resonance serial number.

Iso.

The isotope of the resonance.

Resonance

The resonance assignment or number.

Bound

Shows the atoms to which the assigned atom is bound. Wrong assignments can be indicated by highlighted bound atoms, when an assignment doesn't match an experiment type.

BMRB Mean

The average chemical shift found for the resonance assignment in the BioMagResBank database.

Random Coil

The random coil chemical shift for the resonance assignment.

Type Prob

The probability that the assigned type is correct, based on the chemical shift information. Ranges from 0 ro 1, for low probability to high probability, respectively.

Value

The chemical shift of the resonance in the selected chemical shift list.

SD

The chemical shift of the resonance in the selected chemical shift list.

Max Peak Δ

The maximum peak delta. (????)

Contribs

The number of contributions to the resonance. (????)

Peaks

The {Peaks} tab gives a list of all the peaks and a quality assessment thereof for the selected peak list. Abnormalities in the peak properties are indicated by highlighting the abnormal properties. The highlighting allows the user to quickly assess any problems. Selected peaks can be inspected directly through the Peaks: Selected Peaks popup using the[Show Peaks] button. After making changes to peaks, for example to fix problems, the table needs to be refreshed using the [Refresh Table] button. Note that updating a peak quality report may take some time, as each individual peak has to be checked.

The Assignment: Quality Reports popup (Peaks).

Peak List

Specifies the peak list for which the quality report is displayed.

Peaks table

This table contains all the peaks in the selected peak list and their quality indicators.

#

The serial number of the peak in the peak list

Assignment

The assignment of the peak.

Assign Errors

Lists assignment errors, if any. For example, if a peak has too many bonds they will be listed here.

Location

The location of the peak as a combination of the chemical shifts in the different dimensions, e.g. 0.81 1.23 17.87.

Volume

The volume of the peak. Abnormal values here indicate outliers in the volume of the peak, and could mean that a peak is for example a noise peak with extremely small volume, or an overlapping peak with extremely high volume.

Log Vol Dev

The number of standard deviations that the logarithm of the absolute value of the peak volume is away from the average of all peaks. Abnormal values here indicate outliers in the volume of the peak, and could mean that a peak is for example a noise peak with extremely small volume, or an overlapping or diagonal peak with extremely high volume.

Height

The height of the peak. Abnormal values here indicate outliers in the height of the peak, and could mean that a peak is for example a noise peak with extremely low height, or an overlapping peak with extremely high height.

Log Height Dev

The number of standard deviations that the logarithm of the absolute value of the peak height is away from the average of all peaks. Abnormal values here indicate outliers in the height of the peak, and could mean that a peak is for example a noise peak with extremely low height, or an overlapping or diagonal peak with extremely high height.

F1, F2, F3.... Max Shift Δ

The Maximum delta shift in dimension F1, F2 etcetera. (???)

Refresh Table

Refreshes the table. This action need to be taken every time when a peak has been modified and a new quality report is needed. Note that for large peak lists this may take some time.

Show Peaks

Shows the selected peaks in the Peaks: Selected Peaks popup.