Peak : Peak Lists

Display, Edit and Create Peak Lists

This popup window collects together most of the data that relates to peaks picked within spectra and how they are organised within peak lists. Higher-level information that relates to the spectra or the experiments that generated the data are found elsewhere, in the Spectra and Experiments tables. Each peak list relates to only one spectrum, but a spectrum can have multiple peak lists, although most spectra will normally have only one. Having more than one peak list for a spectrum allows different kinds of peaks to be separated, for example to distinguish between different peak picking techniques or real and synthetic peaks.

This popup window is divided into three tab sections. The first shows all of the peak lists within the current project; the second lists all of the peaks within a selected list and the third allows the user to make artificial or synthetic peak lists based upon things like chemical shift values and coordinate structures.

Peak Lists

This table shows all of the peaks lists within the project, the parameters that relate directly to them and how they fit with the spectrum/experiment hierarchy. Each peak list is identified by the experiment and spectrum to which it belongs, as well as a serial number for the list. Some of the values in the table may be edited to control a peak list’s display and behavior. The most important of these is set in the “Active?” column. Each spectrum may have only one active peak list. The active peak list for a spectrum is the only peak list that will normally be assigned, have its peak selected in the spectrum display and will have newly picked peaks added to it. Inactive peak lists are displayed but do not usually participate in the manipulations that are done via the spectrum windows.

Each peak list may be displayed in a different style, thus this table allows the user to change the symbol and colour of the peak list when it is displayed within spectra. The symbol refers to the cross mark that is placed to indicate the picked position of the peak; usually an extremum in spectrum intensity. The colour of the peak list relates to both the colour of the marker symbols and any textual annotation, e.g. to indicate resonance assignment.

Below the peak list table a few functions that operate on whole peak lists are available. The [Add Sister List] is notable because it allows the user to make a new blank peak list, to which new peaks may be copied or added. Here, the new peak list is added to the same spectrum as the peak list that is currently selected in the table, hence the use of the word “Sister”. The [Copy Peaks] is used to duplicate peaks, from one peak list to another, assuming the spectrum dimensions are compatible in terms of isotope types. The [Shift Whole Peak List] is useful if all of the peaks of a list need to be moved by the same amount relative to their spectrum. This is useful when peaks are imported with an offset, e.g. for matching TROSY and non-TROSY peaks, or if spectrum referencing has changed and peaks have not been properly located.

Peak Table

The idea behind this table is to give a textual listing of all the peaks in the selected peak list. The user can compare and edit peak parameters, e.g in terms of assignment or intensity, and can follow links to other kinds of information. For example the user can go from the selected peaks to the resonances that are assigned to those peaks. Double-clicking on the editable columns of the table allows many of the parameters to be directly edited, although discretion is recommended for certain operations like changing positions and intensity values. The pulldown menu above the peak table allows the user to specify which peak list will be displayed. The “Status” just below may be used to show only a subset of peaks, depending on how they are assigned.

Most of the options above the peak table provide functions that allow the user to locate and mark peaks within the spectrum display windows. The [Strip Selected] and [Find Peak] options are used to find particular peaks that have been selected in the table (with left-click +/- <Ctrl>/<Shift>). The former sub-divides the locations for separate peaks using strips (window dividers) and the latter locates only the last selected peak. The [Strip Locations] and [Go To Position] work in a similar way, except that they use only the position information from the selected peaks and don’t necessarily display the actual selected peaks. The idea here is that peak positions can be used to move the display of any spectrum window that share at least some of the same kind of isotopes on their axes. For example a 2D 15N HSQC peak can be used to find an amide position (H & N) in 3D HNcoCA spectrum, thus locating two out of three axes. This functionality is very useful when some peak lists are used as “roots” to coordinate others.

The buttons below the main peak table allow the user to edit and view many types of data associated with the peaks, although many parameters may be changed by double-clicking in the peak table. Some notable functions include: [Unalias] which is used to move ‘ghost’ peaks to their real underlying ppm values by adding or subtracting a whole number of spectrum widths to their position. This is used when a peak lies outside the normal recorded bounds of the spectrum but nonetheless still appears within it because as an aliased signal; [Assign] opens the Assignment Panel to control which resonances have been linked to the dimensions of the peak; to indicate what caused the peak. Such assignments may be to the resonances of specific atoms or resonances that are currently anonymous; [Deassign] clears all of the resonance assignments to the peak dimensions. This does not affect how the resonances may be connected to atoms; [Set Details] allows the user to set the “Details” column for all of the peaks selected in the table with a single operation; [Propagate Assign] spreads resonance assignments from one peak (the last selected) to the others selected in the table, which is useful even if not all of the peak dimensions are the same type, for example when spreading amide H & N resonances from an HSQC peak to 3D triple-resonance peaks.

Synthetic Lists

The final tab is used to make new peak lists where peak entities are predicted by artificial or synthetic means, i.e. not by direct inspection of spectrum intensities. If possible, peaks that are created by one of the synthetic methods and which are used as a source of evidence for NMR derived information should ultimately be related to the spectrum data; by re-centering the peaks and re-calculating their intensities. Four methods are currently available for synthesising new peak lists:

The “From Shift Intersections” section allows the user to make a peak list based upon the intersection between chemical shifts that occur within the bounds of a given spectrum (the same spectrum that the peak list will belong to). A shift list is selected to specify which chemical shift values are used, and by default this shift list is the one that the spectrum uses during assignment (set at the experiment level). The synthesised peaks will correspond to all chemical shift values that match the spectrum data dimensions, in terms of isotope, and fit together to give a complete peak assignment. This shift matching process also considers whether the spectrum data dimensions represent only atom sites that are directly bound; thus removing many spurious peak locations. For example a 15N HSQC peak list may be made from 1H and 15N resonances that lie along the two spectrum axes of the resonances and are covalently bound to one another. The through-space options control how far predictions are made for transfers like NOESY, i.e. in the absence of a structure you can limit the number of bonds and/or number of sequential residues to consider. It should be noted that this system cannot predict peaks for all kinds of spectra. It is currently limited to those kinds of experiment where all magnetisation transfers go through atom sites that are either recorded directly as a spectrum dimension (e.g. in HNCA, HH NOESY) or are intermediate between two recorded dimensions (e.g. HN(co)CA) and linked via J-coupling or one-bond transfer. More kinds of peak list may be predicted in the future. It is notable that for NOESY peak lists only peaks that represent connections between atoms that are either in the same residue or within five covalent bonds of one another are used.

The “For Shifts and Structure” section makes synthetic peak lists using chemical shift intersections, as described above, but only allowing spectra that have a through-space connectivity (e.g. NOESY) between two of their dimensions. Also when comparing through-space connections, the possible peaks are filtered according to how close assigned atoms are within a structure ensemble. Any peaks that would be assigned to pairs of atoms that are further apart than the “Max Dist” value will not be made. The user can also reject certain peaks by insisting on a minimum spectrum intensity value at its position.

The “From Transposition” section is used to make peaks based upon reflection about a homonuclear diagonal. For example if peaks have been picked on only one side of a 2D NOESY experiment’s diagonal, corresponding duplicates may be made on the other side of the diagonal where the assignments and positions of the two dimensions are swapped. Naturally, this functionality is limited to only spectra that have two data dimensions with of the same isotope type.

The “From Distance Restraints” section is used to recreate NOE and other through-space peak lists based upon distance restraints, which may have been imported from outside CCPN. The individual distance restrains provide a list of atom pairs that are known to be close. The peaks are then synthesised from those by obtaining the chemical shift of the atom’s resonances. Where relevant, the chemical shift of any covalently bound resonances are also obtained. The chemical shifts are then matched within the bounds of the selected spectrum, considering whether any of the data dimensions represent a ‘onebond’ relationship that much be preserved in the peak assignments. It should be noted that a single distance restraint may give rise to more than one peak, when it is not possible to determine which restrained atom goes on which spectrum dimension. Also, ambiguous distance restraints will give rise to ambiguous peak assignments.

Caveats & Tips

If you need the peak positions to be displayed in Hz units or as data point positions, the “Position Unit” pulldown at the top may be changed.

The [Set Details] function can be handy for marking peaks that cause violations in a structure calculation and thus need further attention.

Peak lists may be merged by copying the peaks from one into another, although this takes no account of duplication.

When making synthetic NOESY (or other though-space) peaks, having a residue limit of 1 or 2 will naturally not have an effect if the bond limit is too short, i.e. where the wouldn’t be enough bonds to get to the next residues.

Main Panel

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Peak Lists

A table of all the peak lists within the current CCPN project

Table 1
Experiment The name of the experiment that gave rise to the spectrum & hence contains the peak list
Spectrum The name of the spectrum to which the peak list pertains
List The serial number of the peak list, within its spectrum
Active? Sets whether the peak list is the active one for its spectrum; always “yes” if there is only one list for a spectrum (Editable)
Color The colour to use for the peak cross/symbol and assignment annotation; each list may have a different colour (Editable)
Symbol The kind of symbol (a small cross on screen) used to indicate picked peak locations for the list (Editable)
No. Peaks The number of peaks in the peak list
% Assigned The percentage of peak dimensions in the whole peak list that carry assignments
Synthetic? Whether the peak list is synthetic/simulated; if so, peak assignments in the list have very little influence on chemical shift averages
Details A textual comment for the peak, often user-supplied (Editable)

button Edit Peaks: Show a table of the individual peaks within the selected peak list

button Delete: Delete the selected peak list and all its peaks

button Add Sister List: Add a new, blank peak list in the same spectrum as the selected peak list

button Copy Peaks: Copy the peaks (positions, intensities and assignments) from the selected peak list to another with matching dimensions

button Shift Whole Peak List: Move all of the peaks in the selected peak list by specified offsets for each dimension; offsets are prompted

Peak Table

A table of the individual peaks within one peak list

pulldown Peak List: Select peak list to display peaks from

pulldown Position Unit: Choose whether to display peak positions in ppm, Hz or points

button Strip Selected: Use the positions of the selected peaks to specify strip locations in the selected window

check Find Peak: Locate the currently selected peak in the specified window

pulldown Window: Choose the spectrum window for locating peaks or strips

check Mark Found: Whether to put a cross-mark though peaks found in a given window

pulldown Status: Restrict peak table to only those assigned a certain way

pulldown Structure: Structure to calculate distances from

button Strip Locations: Use the selected peak positions to specify strip positions in a higher dimensionality window.

check Go To Position: Use the selected peak position to navigate to a location in a higher dimensionality window

pulldown *None*: Choose the higher dimensionality spectrum window to use as a navigation & strip target

button Mark Selected: Put multidimensional cross-marks through selected peaks

Table 2
# Documentation missing
Position F1 Documentation missing
Position F2 Documentation missing
Assign F1 Documentation missing
Assign F2 Documentation missing
Height Documentation missing
Volume Documentation missing
Line Width F1 (Hz) Documentation missing
Line Width F2 (Hz) Documentation missing
Merit Documentation missing
Details Documentation missing
Fit Method Documentation missing
Vol. Method Documentation missing

button Add: Add a new peak, specifying its position

button Edit: Edit the position of the currently selected peak

button Unalias: Move the ppm position of a peak a number of sweep withs to its correct aliased/folded position

button Delete: Delete the currently selected peaks

button Assign: Assign the dimensions of the currently selected peak

button Deassign: Remove all assignments from the currently selected peaks

button Set Details: Set the details field of the currently selected peaks

button Set As Current: Set the peaks selected in the table as the ones selected in the spectrum windows

button Resonances: Show a table of resonances assigned to the selected peaks

button Deassign Dim: Deassign a specified dimension of the selected peaks

button Recalc Fit: Recalculate the center, height and line width of the selected peaks

button Recalc Volume: Recalculate the volume of the selected peaks

button Show On Structure: Show the assignment connections of the selected peaks on the selected structure

button Propagate Assign: Spread the resonance assignments of the peak last selected to all selected peaks

button Propagate Merit: Copy the merit value of the last selected peak to all selected peaks

button Propagate Details: Copy the details of the last selected peak to all selected peaks

Synthetic Lists

Tools to generate peak lists by artificial means; from shifts, structures, transposition & restraints

From Shift Intersections

button Predict from shifts: Make a synthetic peak list using the intersection of chemical shift values, according to the specified settings

pulldown Spectrum: Selects which spectrum to make synthetic peaks for; a new peak list is generated

pulldown Isotope Labelling: If required, selects the isotope labelling specification to filter possible chemical shift intersections & hence peak creation

pulldown Shift List: Sets which list to use as the source of chemical shift values; peaks will be made at relevant shift intersections

pulldown Mol System: Allows the considered shifts to be limited to only those assigned to a given molecular system (group of chains)

float 0.25: The minimum spin active isotope incorporation for an atom site and correlation to be considered, according to the selected labelling

check Use unassigned?: Whether to make peaks for chemical shift intersections involving one or more unassigned resonances

pulldown Through-space bond limit: When dealing with through-space transfers like, NOESY or DARR, which atom pairs to include, based on the maximum number if intervening bonds

pulldown Through-space residue limit: When dealing with through-space transfers like, NOESY or DARR, which atom pairs to include based on residue separation

From Shifts and Structure

button Predict from structure: Make a synthetic peak list using structural distance to filter possible chemical shift intersections

pulldown Spectrum: Selects which spectrum to make distance filtered synthetic peaks for; a new peak list is generated

pulldown Isotope Labelling: If required, selects a isotope labelling scheme to apply further filtering for possible chemical shift intersections

pulldown Structure: Selects which structure ensemble to use for calculating atomic distances

float 5.0: Sets the Angstrom threshold below which atoms may be considered for making peaks; if their shift intersection lies in the spectrum bounds

float 0.25: The minimum spin active isotope incorporation for an atom site and correlation to be considered, according to the selected scheme

pulldown Shift List: Sets which chemical shift list to use for generating potential peak locations

float Min Spectrum Value (Height): Selects a threshold for the spectrum intensity at a potential peak location, if the intensity is below the value no peak is made

From Transposition

button Make transpose list: Make a peak list, in the same spectrum as the selected list, where peak positions in homonuclear dimensions are swapped relative to the source

pulldown Source Peak List: Selects which peak list to use as the source of the peak position information; the new peak list will share the same spectrum

From Distance Restraints

button Make from restraints: Make a synthetic peak list using information from a distance restraint list

pulldown Spectrum: Selects which spectrum to make a new peak list in; the experiment for this spectrum states which shift list provides peak locations

pulldown Restraint Set: Selects which set of restraints the input distance restraint list is contained within

pulldown Distance List: Selects which distance restraint list will be used to provide information about which correlations will be made in the new peak list

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