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Ccpnmr Assignment Of Lease

Assignment : NOE Contributions¶

Assign Contributions to NOE Peaks Using Structures and Chemical Shifts

This popup window is designed to assist in the latter stages of assigning NOE and other through-space spectra that are used in the generation of macromolecular structures. The system uses the matching of chemical shifts to peak positions, and a structure if available, to suggest assignments for peaks. Guiding structures are used to eliminate assignment possibilities where the resonances would be too far apart in space to give a contribution to the signal. Such structures may include comparative (homology) models or unfinalised structures from part way though the structure generation process, for example as produced by ARIA or CYANA programs.

User Operation

To operate this tool the user selects a NOESY or other though-space peak list that will be assigned. Various options may be chosen, including how assignment possibilities are displayed on a graphical structure view and what the tolerances are for considering an assignment possibility. The distance tolerance is the maximum allowable separation between potential peak dimension assignments (connected by a through-space transfer) if a guide structure is present. The F1, F2 etc. dimensional isotope tolerances are the maximum allowed chemical shift differences for matching a peak position to a resonance of known chemical shift. The “Navigation Windows” table allows the user to specify which spectrum windows will be used for navigation; to show a selected peak’s location. This table displays all windows that the peak list may be viewed in, and the “Use?” column may be toggled to activate a window for navigation.

In the “Peak Assignments” tab the top table lists all of the peaks that are present in the selected peak list. Clicking on a peak row in this table will cause the lower table to be filled with the assignment possibilities for the peak. If navigation windows and a guide structure display is active selecting a peak in this way will also navigate to the appropriate spot in the spectrum and show structural connections.

Peak assignment possibilities in the lower table are, by default, displayed in a ranked order according to how close the peak position is to the chemical shifts and how distant in space the relevant atoms are in any guide structure. The chemical shift differences are weighted by the per-dimension tolerances so that values from dissimilar isotopes may be combined. A peak assignment is made by selecting the specific row for the resonances you wish to assign to the selected peak and clicking [Assign Selected]. An individual dimension assignment may be removed by clicking on the appropriate cell in the “Possible Assignments” table and clicking [Delete Assignment], or all assignments for the peak may be cleared with [Delete All Assignments].

The [Predict Peaks] function is designed to show you where the listed assignment possibilities would make peaks in the spectrum, given their recorded chemical shifts. This option makes synthetic peak crosses to show where on the spectrum the resonance intersections would be, and if possible what structural distance they represent. From these the user may be able to make a better judgement of which possibilities are likely to cause a peak. Such synthetic peaks are made in an entirely separate peak list to the main one, and their list may be deleted at any time without adverse effect.

Caveats and Tips

The “Tol. Weighted Combined Delta” value in the lower table is a weighted chemical shift distance (structure distance is not included) that can be used an assignment criterion, as long as your shift tolerances are set appropriately. The actual calculation is to take the shift difference for each dimension and divide by the tolerance for that dimension (normalise to be <= 1.0). All dimensions are then combined by taking the square root of the sum of squares, i.e. to give a “shift distance”. The maximum value will be the square root of the number of dimensions.

It should be noted that the [Assign Whole Peak List] will assign all of the possibilities, as listed in the lower table, for all the peaks in the entire peak list. Hence, when using this function it is recommended that suitably narrow distance and chemical shift tolerances are set.

The chemical shift list that is used for matching resonances to peak positions is the one set on the experiment record for the selected peak list.

The experiment record of a peak list must be set as a through-space type (e.g. NOESY) for it to be considered.

This system will work with non-NOESY though-space experiments such as spin diffusion types used for solid-state samples. However, at present assignment contribution fractions are only calculated using the Intensity^(1/6) summation appropriate for NOE experiments.

This system takes no account of missing assignments; resonances that may cause a peak but do not have a known chemical shift.

Main Panel¶

Clone: Clone popup window

Help: Show popup help document

Close: Close popup

Peak List & Display Settings¶

Sets the parameters required for matching peaks to NOE assignments, including which peak list and structure to use

NOE Peak List: Selects which NOE peak list will be considered for the matching of close resonances; in terms of both shift and distance)

Structure Display: Selects which kind of assignment possibilities, for a peak, to display on a graphical structure display

Structure: Selects which structure ensemble will be used for calculating atomic distances within the graphical structure display

Aliased Possible: Sets whether the peaks could be caused by aliased resonances; not at their real ppm value, but a whole number of sweep widths away

Focus Structure: Sets whether to rotate the graphical structure display to focus on the current assignment possibilities

Mark Peak: Sets whether to mark the selected peak position, as displayed in the selected navigation windows

Tolerances¶

8.0: Sets the upper limit for structural distance, below which pairs of close atom sites may be considered for assignment

0.08: The shift scaling factor for dimension 1 (1H); used to give equivalency to ppm distances for different kinds of isotope

0.16: The shift scaling factor for dimension 2 (1H); used to give equivalency to ppm distances for different kinds of isotope

0.8: The shift scaling factor for dimension 3 (15N); used to give equivalency to ppm distances for different kinds of isotope

Navigation Windows¶

Table 1
#The serial number of the spectrum window, which may be used to navigate to NOE peak locations
NameThe name of the spectrum window, which may be used to navigate to NOE peak locations
Use?Sets whether to use the spectrum window for navigation, if so its view will be moved to display the selected peak location (Editable)

Peak Assignments¶

A table of the peaks that NOE assignments are considered for, and their structure & shift filtered assignment possibilities

NOE Peaks¶

Table 2
#The serial number of the peak in its peak list
PositionThe position of the peak in all of its dimensions
AssignmentThe current resonance assignment annotation of the peak
DetailsA textual description of the peak; can be set from the main peak tables, e.g. to mark violated peaks
HeightThe height intensity of the peak; usually from the spectrum data matrix,but possibly set manually
VolumeThe volume integral of the peak; calculated using the method stated in the peak list table

Previous Peak: Selects the previous peak in the table and display NOE assignment possibilities; causes navigation within spectrum windows if this is set

Selected Peak: Selects a peak in the table based upon the peak currently selected in spectrum windows; uses the first if many are selected

Next Peak: Selects the next peak in the table and display NOE assignment possibilities; causes navigation within spectrum windows if this is set

Possible Assignments¶

Table 3
#Rank of assignment possibility; best matching first
Assign F1: 1HThe 1H resonance assignment possibility for dimension 1
Assign F2: 1HThe 1H resonance assignment possibility for dimension 2
Assign F3: 15NThe 15N resonance assignment possibility for dimension 3
DistDistance, in the selected structure, between atom assignment possibilities, for the NOESY linked dimensions
Tol. Weighted Combined &#916;The combined chemical shift difference, for all dimensions & weighted by isotope tolerance, from peak to possible resonance assignment
&#916;F1The chemical shift difference between peak position and resonance assignment for dimension 1
&#916;F2The chemical shift difference between peak position and resonance assignment for dimension 2
&#916;F3The chemical shift difference between peak position and resonance assignment for dimension 3
Contrib FracThe fraction of the total NOE intensity that a committed assignment contributes; assuming NOE intensity proportional to distance to the power of -6
Shift F1The chemical shift of the resonance assignment possibility for dimension 1
Shift F2The chemical shift of the resonance assignment possibility for dimension 2
Shift F3The chemical shift of the resonance assignment possibility for dimension 3

Assign Selected: Assign the peak to the individual resonance+dimension possibility selected in the above table

Delete Assignment: Remove the assignment of the individual resonance+dimension possibility selected in the above table

Delete All Assignments: Delete all resonance assignment for all dimensions of the selected peak

Predict Peaks: Make simulated peaks (in a separate, temporary peak list) at the locations of the displayed resonance intersections

Assign Whole Peak List: Assign all the peaks in the selected peak list to all of their NOE assignment possibilities; only useful if strict tolerances are set

Assignment : Assignment Panel¶

Assign Resonances To Peak Dimensions

The purpose of this popup window is to control the assignment of resonances to a specific, picked, peak in a spectrum. Such resonances might already be associated with a specific atom or they could be anonymous, and only represented by a resonance number e.g. “[123]”.

The general layout of the window is such that you have two tables for each dimension of the cross peak, i.e. the dimensions are represented as separate rows. The first column of tables on the left indicate the resonances which are currently assigned to the peak dimensions. The second column of tables on the right indicate the resonances that might be assigned to the peak dimensions; these are usually ordered according to chemical shift closeness to the peak position in that dimension.

In normal operation to assign the dimension of a peak to a specific resonance by clicking on one of the resonance row from the right hand table for the specific peak dimension. If the resonance is not already assigned, it will appear in the left hand table to indicate that is now assigned. More than one resonance may be assigned to a peak dimension (e.g. for overlapping or ambiguous signals) by clicking on another resonance for the same dimension. Totally new, never seen before, resonances are added to a dimension with the [<New>] option; the new resonance then gains a chemical shift based on this peak dimension position.

Clicking on a resonance row in the left hand tables allows you to remove it as a peak assignment [Clear Dim Contrib] or change the way that the specific resonance is linked to atoms or residue spin systems. The light blue buttons toward the bottom will allow you to add specific atomic assignments, atom type information or tentative assignments. The light orange buttons allow you to remove atomic and residue/spin system assignments.

Various options are given to control which resonance assignment possibilities appear in the right hand tables. Some options show more possibilities, i.e. by considering wider position-to-shift tolerances or including matches outside of the current sweep with. Other options restrict the possibilities, usually to make the selection more relevant to the current situation; you may want only assignments within a given molecular system (group of chains), within a single residue, appropriate for an isotope labelling scheme or those that obey covalent bond relationships of the recorded experiment.

Caveats & Tips

To change the peak that is being assigned in the window move the mouse over the desired peak in a spectrum window and press the “a” key (lower case). The experiment:spectrum identity of the peak is indicated at the top left.

Only resonances that are within the chemical shift tolerances (set per spectrum dimension) will be shown as assignment possibilities. The chemical shift value used for each resonance is taken from the shift list for the peak’s experiment.

Distances only appear in the tables if you have an appropriate structure set at the top and then only if there are through-space transfers in particular dimensions of the peak’s experiment.

“Assignment Groups” are only used when you wish to specify mutually exclusive assignment possibilities, e.g. when you have an NOE peak caused by two signals and only certain assignments go together. Resonances with the same group number go together and those with different numbers do not mix; so you would not get an inappropriate distance restraint for example.

Main Panel¶

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