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Assignment : NOE Contributions
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**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.

**Reciprocal Return Peaks**

The active windows can not only display the location of a selected peak, but
also a series of strips (window sub-divisions) that relate to any reciprocal,
symmetry related (return) peaks. This is useful for the resolution of
assignment ambiguity. If a peak is thought to be due to an NOE from resonance
A to resonance B a reciprocal NOE (from B to A) will usually be present to
confirm the assignment possibility, assuming the return peak would be visible
in the spectrum. If strips for return peaks are required the user should
select the "Strip Return Peaks" option at the top of the settings tab.

**Peak Assignments**

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 "Strip Return Peaks" option will override any existing strips within the
selected spectrum windows. If the windows should not be affected in this way
the option should be switched off.

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
==========

|button| **Clone**: Clone popup window

|button| **Help**: Show popup help document

|button| **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

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

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

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

|check| **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

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

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

Tolerances
~~~~~~~~~~


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

Navigation Windows
~~~~~~~~~~~~~~~~~~


===========  =======================================================================================================================================
**Table 1**
----------------------------------------------------------------------------------------------------------------------------------------------------
        *#*  The serial number of the spectrum window, which may be used to navigate to NOE peak locations 
     *Name*  The 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 
  *Position*  The position of the peak in all of its dimensions 
*Assignment*  The current resonance assignment annotation of the peak 
   *Details*  A textual description of the peak; can be set from the main peak tables, e.g. to mark violated peaks 
    *Height*  The height intensity of the peak; usually from the spectrum data matrix,but possibly set manually 
    *Volume*  The volume integral of the peak; calculated using the method stated in the peak list table 
============  =================================================================================================================



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

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

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

|button| **Find Reciprocal Peaks**: Display strips for possible (symmetry related) NOE reciprocating return peaks, e.g. for an A-B peak look for possible B-A peaks.

Possible Assignments
~~~~~~~~~~~~~~~~~~~~


==========================  =======================
**Table 3**
---------------------------------------------------
                       *#*  *Documentation missing* 
                *Reson F1*  *Documentation missing* 
                *Reson F2*  *Documentation missing* 
                *Reson F3*  *Documentation missing* 
                *Reson F4*  *Documentation missing* 
                   *Dist.*  *Documentation missing* 
*Tol. Weighted Combined Δ*  *Documentation missing* 
                     *ΔF1*  *Documentation missing* 
                     *ΔF2*  *Documentation missing* 
                     *ΔF3*  *Documentation missing* 
                     *ΔF4*  *Documentation missing* 
   *Contrib Frac.Shift F1*  *Documentation missing* 
                *Shift F2*  *Documentation missing* 
                *Shift F3*  *Documentation missing* 
                *Shift F4*  *Documentation missing* 
==========================  =======================



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

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

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

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

|button| **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

