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Analyses of Potential Errors and Completeness in Assignment
This popup presents a series of tables that enables the user to get a sense of how complete the assignment is within a given project and whether there are any assignments which look like they might be mistakes. This system is not designed to say that something is definitely missing or definitely a mistake, but rather tries to focus attention to any places where there may potentially be a problem. Often something that is highlighted in red as “unusual” merely needs checking, to ensure that the user has a good explanation. The layout consists of four tabs, each relating to a different aspect of assignment.
Atom Assign Status
The first tab contains various categories of atom, from the selected molecular system, like “backbone” or “Lys” (for amino acid type lysine). Each category has an indication of how many, out of the total available for that type, have been assigned and what chemical shift range they cover. This kind of information is useful to track the assignment progress of a project and to give a final summary. By default the table represents the atoms in the whole of the selected molecular system, but the user may specify only a subset by typing the appropriate chain letters and residue ranges into the “Residue Selection” field.
Through-Space Status
The second tab contains a table that gives the counts of various classes of through-space connection, e.g. for NOESY experiments. Counts are given on a per-chain and per-residue basis. In this way the user can gauge the information density that has been or may be used during structure calculation. By default the table shows data for all peak lists that have and experiment type that is deemed to be “through-space”, like NOESY or solid-state dipole-dipole. Data may be displayed for only one of these peak lists by selecting from the “Peak List” pulldown menu.
Resonances
The third table considers all of the resonances that carry chemical shifts in a specified shift list. The purpose of this table is to indicate potential problems with assignment from the perspective of a resonance, rather than peaks, which are covered in the next tab. Three basic category of error are highlighted (and appear as red cells):
The user may eliminate rows from the table which do not carry any warnings by selecting the “Show only alerts” option.
Peaks
For a selected peak list, the forth table displays assignment and intensity problems on a per-peak basis. Two basic kinds of check are made for each peak:
The user may eliminate rows from the table which do not carry any warnings by selecting the “Show only alerts” option.
Caveats & Tips
Because the analyses are relatively slow to perform the tables will not automatically update every time there is an assignment change. If significant changes have been made and the tables need to be updated the user can click the [Update Table] button to force a refresh.
The [Show Peaks] and [Show Resonances] buttons can be used to display all of the peaks and resonances, in tabular form, from which the information in the selected rows are derived. These options are not available for the first tab.
Lots of red warnings in the “Resonances” tab, especially in in the “Bound” column, may be an indication of a problem with the specification of one or more experiment types, rather than a direct problem with the peak assignments. Knowledge of which experimental dimensions represent ‘onebond’ transfers, by virtue of peak assignment, indicates which atomic assignments are in a covalent bond context. The most common mistakes in this regard are the incorrect choice of experiment type or an incorrect choice of dimension order (i.e. how the real experiment dimensions map to the CCPN reference). Both of these problems may be fixed by considering the “Experiment Types” tab in the Experiments popup window. Here, most dimension order problems are fixed by editing the “Transfers To Dim” column in the lower left table, using the user’s knowledge of how the dimensions are connected/correlated.
Documentation missing
Mol System: Selects which molecular system (group of chains) to display assignment status information for
Shift List: Selects which shift list is used as the source of chemical shift information
Residue Selection: Sets which chain and range of residues to show assignment status for, e.g. “2-10, 13-77” or “A1-99, B20-120”
Table 1 | |
Category | The name of a category into which atoms of the selected chain/residue have been grouped |
Available | The total number of atoms (or equivalent sets for methyl groups) that are available for assignment within the category |
Assigned | The number of atoms (or equivalence groups) that have actually been assigned within the category |
% Assigned | The percentage of available atoms (or equivalence groups) hat have been assigned within the category |
Min Shift | The lowest chemical shift value of the assigned atoms within in the category |
Mean Shift | The average chemical shift value of the assigned atoms within in the category |
Max Shift | The highest chemical shift value of the assigned atoms within in the category |
Documentation missing
Mol System: Selects which molecular system (group of chains) to show through-space connectivity information for
Peak List: Selects which through-space peak list(s) to show connectivity information for
Table 2 | |
Seq Element | The identity of the chain or residue that the data in the row pertains |
Total | The total number of though-space connections for the chain/residue in the selected peak list(s) |
Intra Residue | The number of connections that lie within a single residue; do not cross between different residues |
Inter Residue | The number of connections that cross from one residue to another |
Sequential | The number of connections between residues that are sequential neighbours |
Short Range | The number of connections between residues that are within four sequence positions of one another |
Short Non-seq | The number of connections between residues that are not sequential neighbours but are within four sequence positions of one another |
Long Range | The number of connections between residues that are five or more sequence positions apart |
Intra Chain | The number of connections that lie within a single molecular chain |
Inter Chain | The number of connections that cross between different molecular chains |
Contacted Residues | For a given residue, a list of sequence numbers for all other residues that are connected |
Documentation missing
Shift List: Selects which shift list to derive chemical shift values from in the resonance analysis
Show only alerts: Sets whether to show only rows in the table for resonances that carry warnings
Table 3 | |
# | The serial number of the resonance |
Iso. | The nuclear isotope type of the resonance |
Resonance | The assignment annotation for the resonance; just its serial number in square brackets if unassigned |
Bound | The assignment annotations of all the other resonances that are considered covalently bound; either by virtue of atom assignments or “onebond” linked experimental dimensions |
BMRB Mean | When atom assigned, the average chemical shift for the atom type given in BioMagResBank data |
Random Coil | When atom assigned, the sequence-adjusted random coil chemical shift value for the atom type |
Type Score | When atom assigned, a score indicating how well the resonance chemical shift fits with the known distribution of shifts for the atom type |
Value | The chemical shift value of the resonance, in the selected shift list |
SD | The standard deviation of the chemical shift value; over the peak dimensions to which the resonance is assigned |
Max Peak Δ | The maximum difference in the averaged chemical shift value and a peak dimension assigned to the resonance |
Dim Contribs | The number of peak dimensions the resonance is assigned to |
Documentation missing
Peak List: Selects which peak list to show peak analyses for
Show only alerts: Sets whether to show only rows in the table for peaks that carry warnings
Table 4 | |
# | The serial number of the peak in the selected peak list |
Assignment | The resonance assignment annotation of the peak |
Assign Errors | Any error that relate to the peak’s resonance assignment |
Location | The position of the peak, in the units of the experimental axes; usually ppm |
Volume | The integration volume of the peak; colour indicates deviation from the peak list average on a logarithmic scale |
Log Vol Dev | The standard deviation of the peak integration volume on a logarithmic scale; highlights strong/weak outliers (which could be genuine) |
Height | The height intensity of the peak; colour indicates deviation from the peak list average on a logarithmic scale |
Log Height Dev | The standard deviation of the height intensity on a logarithmic scale; highlights strong/weak outliers (which could be genuine) and inappropriate peak sign |
Update Table: Manually update the currently viewed table in light of assignment changes etc.
Show Peaks: Show a table of the peaks that relate to the selected rows, either directly or by virtue of assignment (depending on the current table)
Show Resonances: Show a table of resonances that relate to the selected rows, either directly or by virtue of assignment (depending on the current table)