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Data Analysis : Heteronuclear NOE
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**Calculate Heteronuclear NOE Values From Peak Intensities**

The purpose of this popup window is to calculate the heteronuclear NOE for
amide resonances based upon a comparison of the peak intensities in spectra
that derive from an NOE saturated experiment and an unsaturated (reference)
experiment. The basic idea of this tool is that three peak lists are chosen,
two of which are for heteronuclear NOE experiments (H,N axes); unsaturated
reference and saturated, and one which is the source of assignments and peak
locations. This last "Assignment" peak list may be the same as one of the NOE
peak lists, but may also be entirely separate.

The "Assignment" peak list is used to specify which peak assignments and
locations should be used for the calculation of the heteronuclear NOE values,
and thus can be used to specify only a subset of the resonances for
measurement. For example, it is common to copy an HQSC peak list for use as
the "Assignment" peak list but remove overlapped and NH2 peaks so that the NOE
values are only calculated for separated backbone amides. The calculation
process involves taking each of these assigned peaks and finding peaks with
the same assignment in the NOE peak lists, or if that fails finding peaks with
a similar position (within the stated tolerances); new peaks may be picked if
the "Pick new peaks?" option is set.

The first "Peak Lists & Settings" tab allows the user to choose the peak lists
and various options that will be used in the peak-finding and NOE calculation.
The "Peaks" table allows the peaks from each of the three peak list selections
to be displayed when one of the "Show" buttons is clicked. The [Separate Peak
Table] function allows these peaks to be displayed in the main, separate `Peak
Lists`_ table, which has many more peak manipulation options. The options
below the table may be used to locate selected peaks within the spectrum
window displays.

The second "Peak Intensity Comparison" tab is where the heteronuclear NOE
values are actually calculated. Assuming that two NOE experiment peak lists
have been chosen and that some of their peaks match the assigned peak
positions then the peak intensities are extracted and NOE values automatically
calculated when the tab is opened. Although, a refresh of the table can be
forced with [Find Matching Peaks] at the bottom

If pairs of NOE saturated and reference peaks are found then the actual
heteronuclear NOE value is displayed as the "Intensity Ratio" in the last,
rightmost, column of the table. To store these values as a NOE measurement
list; so that the data can be saved in the CCPN project without need for
recalculation, the [Create Hetero NOE List] function can be used. The results
are then available to view at any time via the `Measurement Lists`_ table.

**Caveats & Tips**

Erroneous peak intensity comparisons may be removed with the [Remove Pairs]
function, but its is common to curate the "Assign" peak list first and
avoid tidying afterwards.

The "Closeness score" can be used to find peak positions where the compared
NOE peaks are unexpectedly far from one another.

.. _`Peak Lists`: EditPeakListsPopup.html
.. _`Measurement Lists`: EditMeasurementListsPopup.html



Main Panel
==========

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

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

|button| **Close**: Close popup

Peak Lists & Settings
=====================

*Documentation missing*

|pulldown| **Ref Peak List**: Selects which peak list is considered the NOE intensity reference (no saturation)

|pulldown| **Sat Peak List**: Selects which peak list is considered as NOE saturated.

|pulldown| **Assignment Peak List**: Selects a peak list with assignments to use as a positional reference

|float| **0.02**: 1H ppm tolerance for matching assigned peaks to reference & NOE saturation peaks

|float| **0.1**: 15N ppm tolerance for matching assigned peaks to reference & NOE saturation peaks

|check| **Pick new peaks?**: Whether to peak new peaks in reference & NOE saturated lists (at assignment locations)

|check| **Assign peaks?**: Whether to assign peaks in the peaks in the reference & NOE saturation lists, if not already assigned

|pulldown| **Intensity Type**: Whether to consider peak height or volume in the heteronuclear NOE calculation

Peaks
~~~~~


|button| **Show Ref Peaks**: Show the selected intensity reference peaks in the below table

|button| **Show Sat Peaks**: Show the selected NOE saturation peaks in the below table

|button| **Show Assign Peaks**: Show the selected assigned peak list in the below table

|button| **Separate Peak Table**: Show the displayed peaks in a separate peak table, where assignments etc. may be adjusted

=============  ===================================================================================================
**Table 1**
------------------------------------------------------------------------------------------------------------------
   *Spectrum*  Experiment:spectrum of peak 
       *List*  Peak list number 
       *Peak*  Peak serial number 
     *Height*  Magnitude of spectrum intensity at peak center (interpolated), unless user edited  *(Editable)*
     *Volume*  Integral of spectrum intensity around peak location, according to chosen volume method  *(Editable)*
      *Merit*  Figure of merit value for peak; zero: "bad" one: "good"  *(Editable)*
    *Details*  User editable textual comment for peak  *(Editable)*
 *Fit Method*  Method used to fit the peak location  *(Editable)*
*Vol. Method*  Method used to calculate the peak volume integral  *(Editable)*
=============  ===================================================================================================



|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

|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

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

Peak Intensity Comparison
=========================

*Documentation missing*

=================  =====================================================================================================
**Table 2**
------------------------------------------------------------------------------------------------------------------------
              *#*  Row number 
       *Sat Peak*  Assignment annotation for NOE saturation peak 
       *Ref Peak*  Assignment annotation for reference peak (no saturation) 
     *1H shift A*  1H chemical shift of NOE saturation peak 
     *1H shift B*  1H chemical shift of reference peak 
    *15N shift A*  15N chemical shift of NOE saturation peak 
    *15N shift B*  15N chemical shift of reference peak 
*Closeness Score*  The separation between compared peaks: square root of the sum of ppm differences squared 
    *Intensity A*  The intensity if the NOE saturation peak 
    *Intensity B*  The intensity of the reference peak (no saturation) 
*Intensity Ratio*  Ration of peak intensities: saturated over reference 
=================  =====================================================================================================



|button| **Refresh Table**: Force a manual update of the table; pair-up NOE saturation and reference peaks according to assigned peak positions

|button| **Remove Pairs**: Remove the selected rows of peak pairs

|button| **Show Peak Pair**: Show peaks corresponding to the selected row in a table

|button| **Create Hetero NOE List**: Save the Heteronuclear NOE values in the CCPN project as a data list

