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Assignment : Copy Assignments
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.. |check| image:: ../images/check.png
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.. |radio| image:: ../images/radio.png
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.. |float| image:: ../images/float.png
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.. |int| image:: ../images/int.png
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.. |entry| image:: ../images/entry.png
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.. |button| image:: ../images/button.png
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.. |selector| image:: ../images/selector.png
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**Copy Resonance Assignments to Different Peak Lists or Molecules**

This popup has two separate but related purposes: firstly, to transfer
resonance assignments from one peak list to another peak list where the peaks
are in similar, but not identical, positions; secondly, to move or duplicate
resonances that are assigned to atoms in one molecular chain to another of
similar sequence.

**Copying Assignments Between Peak Lists**

The general idea of the first tab is to select two peak lists, one of which
acts as the "source" where resonance assignments are copied from and another
to act as the "target" where assignments are copied to. In general both the
source and targets peak lists will be from experiments with the same number
and kinds of axis. However, it is also possible to copy assignments *to* a
target peak list that is of *lower* dimensionality than the source. For
example you can copy 3D 15N HSQC-NOESY (H,N,H dimensions) assignments to
15N-HSQC (H,N dimensions) or 2D NOESY (H,H dimensions), and in these cases
only resonance assignments that go on dimensions common to source and target
will be transferred.

The "Source Peaks" table lists all the peaks that assignments may be copied
from, together with an indication the number of peaks that are close and the
one that is closest. The "Target Peaks" table is updated for an individual
source peak when you click on a row of the "Source Peaks" table; to show you
details of all the peaks that match in terms of position.

The matching of peak positions is made according to a chemical shift distance
measure and only possibilities that lie within the distance threshold are
considered. The chemical shift distance is calculated by taking the difference
in peak positions for each dimension, dividing each difference by the scale
factor for the isotope that appears on that dimension, squaring the
differences and taking the square root of their summation. The isotope scale
factors, which you can set in the interface mean that differences in
dissimilar dimensions can be compared. By default the distances can be thought
of in terms as the "1H" equivalent.

If suitable matches are found, resonance assignments are copied between peaks
either on an individual basis, by selecting the required target in the lower
table and using [Assign Selected Target], or *en masse* by using the other
buttons which process all of the peaks in the list; copying assignments if there
is only a single matching target within the distance threshold, or
to the  closest matching target. When using the process-all functions it is
common to start with a very strict/short threshold radius, assign some peaks
and then increase the threshold to consider the poorer matching ones.

**Copying Assignments Between Molecular Chains**

The second tab is used to move resonances' atomic assignments to a different
molecule/chain, while maintaining assignments to peaks. When copying
assignments between molecular chains, i.e. the entities  with residues and
atoms that you assign, the general principle is that you choose one chain as a
source, to get assignments from, and another as a target, to transfer
assignments to. Chains may have identical sequences, for example when copying
assignments within a homodimer, or reasonably different sequences. In the
latter case a pairwise sequence alignment is used to determine the initial
mapping between source and target residues.

With the chain selection setup, the next task is usually to consider how
moving assignments will affect the peaks that the source chain resonances are
assigned to. In this regard there are three options and they are all specified
on a per-experiment basis (and thus affect that experiment's spectra and
peaks). The first option is to leave an experiment alone ("don't move") so
that its peaks are not affected at all. The second option is to move to the
target, whereby all resonance assignments on the peaks are moved to the other
chain. The third option is to duplicate assignments on the peaks so that they
are assigned to both the source and the target chains; this makes each peak
assigned to double the number of resonances. If a resonance is moved entirely
to the target chain (no peaks left at source) then the resonance's atomic
assignment is simply pointed to the different chain. If a resonance remains
partly assigned to the original chain, then a new resonance is made and this
is the one assigned to the target chain; the old resonance remains on the
source chain.

Where residues don't match exactly between the two chains, any resonances
assigned to atoms with no direct equivalent (nothing of the same name) will
still be copied across; their spin system will become the target residue, they
retain their original atom types, but they will not have full atomic
assignments. If the destination residue does not appear correctly in the lower
table, the user may change the residue-residue mapping by double clicking in
the "Destination" column.


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

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

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

|button| **Close**: Close popup

Between Peak Lists
==================

*Documentation missing*

Options
~~~~~~~


|pulldown| **Source Peak List**: Selects the peak list to copy assignments from

|pulldown| **Target Peak List**: Selects the peak list which will be assigned

|check| **Show Already Copied?**: Whether to show source peaks in the table whose assignments are already copied

|check| **Overwrite Assignments?**: Whether to overwrite any existing assignments in the target peak list

|check| **Follow Peaks?**: Whether to follow the location of peaks in the spectrum window when clicking on a peak row

|check| **Only Good Matches?**: When selected only source peaks with at least one good target match will be shown, otherwise all source peaks are shown

|check| **Consider Aliased?**: Whether target peaks could be aliased; position matching can add whole numbers of sweep widths

|pulldown| **Follow Window**: Selects which spectrum window will be used to navigate to source & target peak positions

|float| **0.08**: The ppm search radius to match peak positions. Note spectrum dimensions will be weighted by the isotope scale factors

Scale Factors
~~~~~~~~~~~~~


|float| **1.0**: The scaling factor used to weight ppm distances in 1H dimensions; used in position radius search

|float| **5.0**: The scaling factor used to weight ppm distances in 15N dimensions; used in position radius search

|float| **10.0**: The scaling factor used to weight ppm distances in 13C dimensions; used in position radius search

Source Peaks
~~~~~~~~~~~~


===================  ==========================================================================================
**Table 1**
---------------------------------------------------------------------------------------------------------------
                *#*  Serial number of the source peak 
       *Assignment*  Assignment of source peak; which will be copied 
     *Num. Matches*  The number of target peaks that match the source peak within the ppm distance 
*Closest Distance.*  The smallest, isotope weighted, ppm distance to a target peak 
       *Best Match*  Assignment annotation of closest matching target peak 
===================  ==========================================================================================



Target Peaks
~~~~~~~~~~~~


============  ====================================================================================================
**Table 2**
------------------------------------------------------------------------------------------------------------------
         *#*  Serial number of target peak possibility 
*Assignment*  Assignment of the target peak, which may be overwritten 
  *Distance*  Isotope weighted (by scale factor per dimension) ppm distance between source and target 
============  ====================================================================================================



|button| **Assign Selected Target**: Copy assignments from the selected source peak to the selected target

|button| **Assign All Singly Matched**: Process all source peaks and copy assignments to those that match a single target within the search radius

|button| **Assign All To Closest**: Process all source peaks and copy assignments to the closest matching target peak (if there is one in the search radius)

Between Molecule Chains
=======================

*Documentation missing*

Options
~~~~~~~


|pulldown| **Source Chain**: Selects the molecular chain from which atom assignments will be copied

|pulldown| **Target Chain**: Selects the molecular chain which will receive new atom assignments

Peak Assignment Transfers
~~~~~~~~~~~~~~~~~~~~~~~~~


============  ======================================================================================================================================
**Table 3**
----------------------------------------------------------------------------------------------------------------------------------------------------
         *#*  Serial number of experiment to consider 
*Experiment*  Name of experiment to consider 
 *Operation*  Sets whether atom assignments for an experiment will be transferred entirely, duplicated on both chains or left unaltered  *(Editable)*
============  ======================================================================================================================================



|button| **Don't Move**: Sets the selected experiments so that their assignments will be left unaltered

|button| **Move to Target**: Sets the selected experiments so that their assignments will be transferred entirely to the target chain

|button| **Duplicate**: Sets the selected experiments so that their assignments will be duplicated for both source and target chains

========================  ========================================================================================
**Table 4**
------------------------------------------------------------------------------------------------------------------
                *Source*  The residue from which assignments may be copied 
     *Source Resonances*  The number of resonance assignments currently on the source residue's atoms 
           *Destination*  The residue in the target chain to which assignments may be copied  *(Editable)*
*Destination Resonances*  The number of resonance assignments currently on the target residue's atoms 
========================  ========================================================================================



Residue Mapping
~~~~~~~~~~~~~~~


|button| **Copy Assignments!**: Go ahead and copy assignments between chains using the selected options

|button| **Enable Selected**: Enable copying of assignments for the selected residues

|button| **Disable Selected**: Disable copying of assignments for the selected residues

