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Data Analysis : Shift Differences
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**Measure Differences Between Pairs of Chemical Shifts**

This system is designed to calculate the differences between pairs of chemical
shift values in two contexts: firstly directly comparing peak locations in
related spectra and secondly by comparing averaged chemical shift values
(averaged over potentially many peak locations) in two different shift lists.
The former allows the comparison to be restricted to only certain peaks, i.e.
those with common assignments in two peak lists, and gives an overall 'shift
distance' for each peak, rather than just differences for the separate
dimensions.

**Peak List Comparison**

Comparing peak positions is achieved with the functions presented in the first
tab. In essence, the user selects two peak lists from the top pulldown menus
and views the results in the table below. The "Atom Names" options allow the
comparison to be restricted to only certain kinds of assignment. (The atom
names have to be complete, no wild cards are allowed.)  The "Scale Factor"
values are used in the calculation of the "Shift Sum" and "Shift Dist" values
so that positional differences in dimensions with dissimilar isotopes may be
compared; the difference for a dimension is multiplied by the scale factor
for its isotope type.

**Shift List Comparison**

The second tab simply takes two chemical shift lists, specified in the
top pulldown menus and compares the values of the contained chemical shifts.
Each row corresponds to one resonance that has a shift measurement in the
two shift lists. The user may optionally filter the list by adding specific
"Atom Names" so that only certain kinds of assigned resonance are compared.
(The atom  names have to be complete, no wild cards are allowed.) It should
be noted that the values in shift lists are typically based upon an average
of the assigned peak positions for resonances that use that list.  Two
different sets of experiments may be compared by allocating them among two
separate shift lists; see the main Experiments_ option.

**Sequence Alignments**

When comparing peak lists or shift lists where assignments are made to two
different but similar chains, the calculations can optionally use a sequence
alignment. The sequence alignment that is used is presented in the third tab
and represents a residue to residue mapping. Which chains are used in the
alignment is automatically determined from those that are assigned in the
selected peak lists or shift lists and at present only the highest scoring
pair of sequences is considered. More fine-grain control may be added in the
future.

**Function Buttons**

The lower function buttons relate to either the peak list or shift list
comparison, depending on which is currently viewed. The [Make Shift
Difference List] is handy to give a permanent record, stored in the CCPN
project, of the calculated chemical shift differences. The shift  difference
lists are a kind of measurement list and are viewable at any time via the
`Measurement Lists`_ table. If a measurement list is not made the only way to
get the same shift differences again is to repeat the calculation. The [Show
On Structure] is designed to colour a graphical structure display so that the
size and colour of atoms is determined by the shift difference of their
resonances - atoms without a shift difference are left at their default
rendering.

**Caveats & Tips**

For investigating how chemical shifts differ when considering more than two
peaks, e.g. when following how peaks move during a titration the
`Follow Shift Changes`_ tool should be used.

To make a peak list that is based on averaged chemical shift values, which may
be compared by this system, then for certain types of spectra the user may
create a synthetic peak list. This is accessed via the `Peak Lists`_ popup
option [Predict from Shifts].

.. _`Follow Shift Changes`: FollowShiftChangesPopup.html
.. _`Peak Lists`: EditPeakListsPopup.html
.. _Experiments: EditExperimentPopup.html
.. _`Measurement Lists`: EditMeasurementListsPopup.html



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

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

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

|button| **Close**: Close popup

Peak List Comparison
====================

Measure differences in chemical shifts by comparing peak positions

Options
~~~~~~~


|pulldown| **Peak List A**: First peak list to use in comparison

|pulldown| **Peak List B**: Second peak list to use in comparison

|check| **Fully assigned only**: Whether to compare positions for only fully assigned peaks

|entry| **H,H1**: Restricts the comparison to peaks assigned to particular kinds of atoms, in their first dimension

|entry| **N**: Restricts the comparison to peaks assigned to particular kinds of atoms, in their second dimension

|check| **Use Sequence Alignment**: Whether to use the residue sequence alignment in the shift comparison

|float| **1.0**: First dimension scaling factor use to compare shifts of dissimilar isotopes

|float| **0.15**: Second dimension scaling factor use to compare shifts of dissimilar isotopes

============  =========================================================================================
**Table 1**
-------------------------------------------------------------------------------------------------------
*Residue(s)*  The residue assignment(s) of the peaks 
  *Reson. 1*  Resonance assignment in the first dimension 
  *Shift 1A*  Chemical shift of first peak (A) in first dimension 
  *Shift 1B*  Chemical shift of second peak (B) in first dimension 
 *Δ 1 (ppm)*  Chemical shift difference in ppm for first dimension 
  *Reson. 2*  Resonance assignment in the second dimension 
  *Shift 2A*  Chemical shift of first peak (A) in second dimension 
  *Shift 2B*  Chemical shift of second peak (B) in second dimension 
 *Δ 2 (ppm)*  Chemical shift difference in ppm for second dimension 
 *Shift Sum*  Sum of the chemical shift differences in the two dimensions 
*Shift Dist*  The square root of the sum of the isotope weighted shift differences squared 
   *Seq Num*  Sequence number of any assigned residue (for easy graphing) 
============  =========================================================================================



Shift List Comparison
=====================

Measure differences in the chemical shift values from two shift lists

|pulldown| **Shift List A**: First chemical shift list used in comparison

|pulldown| **Shift List B**: Second chemical shift list used in comparison

|check| **Use Sequence Alignment**: Whether to use the residue sequence alignment to compare dissimilar molecules

|entry| **Atom Names**: Restricts the comparison to only specific atom types, e.g. "HA, HB"

=============  ==================================================================
**Table 2**
---------------------------------------------------------------------------------
         *#1*  Serial number of first resonance 
         *#2*  Serial number of second resonance 
*Assign Name*  Assignment of resonance(s) 
  *Residue 1*  Residue assigned to first resonance 
  *Residue 2*  Residue assigned to second resonance 
    *Shift 1*  Chemical shift value of first resonance 
    *Shift 2*  Chemical shift value of second resonance 
          *Δ*  Chemical shift difference, in units of the shift list 
=============  ==================================================================



Sequence Alignment
==================

The sequence alignment used to compare shifts between two different molecules

====================  =========================================================================
**Table 3**
-----------------------------------------------------------------------------------------------
           *Residue*  Residue in the first sequence 
   *Aligned Residue*  Aligned residue in the second sequence 
*Common Assignments*  Names of atom assigned resonances common to aligned residues 
====================  =========================================================================



|button| **Show Peaks**: Show a table of peaks corresponding/assigned to the selected rows

|button| **Update**: Force a manual refresh of the shift difference calculation

|button| **Make Shift Difference List**: Save the results in the CCPN project as a data list

|button| **Show On Structure**: Show the shift difference results on a graphical structure display

