========================
Chart : Assignment Graph
========================


.. |pulldown| image:: ../images/pulldown.png
   :align: bottom


.. |check| image:: ../images/check.png
   :align: bottom


.. |radio| image:: ../images/radio.png
   :align: bottom


.. |float| image:: ../images/float.png
   :align: bottom


.. |int| image:: ../images/int.png
   :align: bottom


.. |entry| image:: ../images/entry.png
   :align: bottom


.. |button| image:: ../images/button.png
   :align: bottom


.. |ramp| image:: ../images/ramp.png
   :align: bottom


.. |selector| image:: ../images/selector.png
   :align: bottom


**Graphical Display of Assignments and Connections**

This popup window is designed to give a graphical display of the atom sites
available in a given molecular chain. In this regard an atom site is a
position along the side chain or scaffold of a residue, like the "beta"
position in  amino acids, or the "three prime" position in nucleic acids.
Accordingly, each atom site represents a carbon or nitrogen atom *and* any
bound hydrogens. Representing atom sites rather than individual atoms provides
an alternative to the `Atom Browser`_ with less clutter but still with
sufficient information to give a clear indication of assignment status, and
in this particular case, of assignment connectivity between atom sites

The layout involves two tabs, one on the left contains the actual graphical
display of the atom sites with assignments, the right "Options" tab  specifies
the details of how to display things; spectrum connections, atom sites and
residues to include.

In normal operation the user starts by slecting the appropriate molecular
chain in the first tab; labelled symbols will appear to display the available
atom sites. The user then switches to the "Options" tab and chooses which
spectra, atom sites and residue types to display. Moving back to the first tab
the user will see that the symbols of assigned atom sites are circled, with a
colour appropriate to the spectrum they are assigned within. Also, if the
selected spectra contain assignments that link different atom sites the
graphical display will include lines that connect the atom site symbols. The
user may use the "Connection Type" pulldown menu to display different kinds of
connectivity lines. By default the displyed connectivity is "Within 4
Residues". Having more than one set of spectrum massignments and connections
displayed at the same time is possible, but this may obscure information in
the chart.

The background colour of the atom set symbol (a labelled circle) is normally
determined according to whether there are *any resonance assignments* to that
site, considering all spectra; black indicates assigned and grey unassigned.
If the user chooses an isotope labelling scheme/pattern in the "Options" tab,
then this black/grey indicator is replaced by colours which represent the
amount of spin-active isotope incorporation at the atom site, according the
scheme or molecule patterns. The various options in the "Isotope Labelling"
section control which colours to use, whether to use only two colours or a
gradient, which isotope is considered (e.g. usually 13C or 1H) and what the
minimum incorporation is for something to be considered as labelled.

**Caveats & Tips**

Clicking with the left mouse button on any of the atom site symbols for a
residue will toggle the activation for the whole residue; flipping between the
greyed-out incative state, that shows no assignments or connections, and the
fully active state.

Right click with the mouse over the main chart to save the graphical display
as a PostScript image, which maye be printed or manipulated in an external
program.

The colours of the spectrum toggle buttons in the "Options" tab is determined
by the positive contour colour for the relevant spectrum. If the spectrum uses
a multicolour scheme the colour used is one from about two thirds of the way
through the scheme.

.. _`Atom Browser`: BrowseAtomsPopup.html



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

|button| **Update**: Manually trigger a redraw of the main chart, in light of new assignments etc

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

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

|button| **Close**: Close popup

Assignment & Connections Chart
==============================

Shows a chart illustrating selected atom groups for a given sequence, their assignment status and connections between them

|pulldown| **Chain**: Selects which molecular chain to display the residue and atom groups for

|pulldown| **Connection Type**: Restricts the assignment connection lines to atom groups with particular sequential relationships


Options
=======

Allows specification of which atoms, residues and spectrum information to use

Spectra
~~~~~~~


|check| **Include predicted peak lists**: Whether to include predicted peak lists in graph

|selector| ***None***: Toggles individual spectra on and off in tha chart; when set on a spectrum will be used to highlight atom groups assigned and connected in that spectrum

Atoms Shown
~~~~~~~~~~~


|selector| ***None***: Toggles particular kinds of atom group on and off in the chart (for all residues with that kind of group) 

|button| **Set1 Atoms**: Switches on assignment display and connections for atoms in "set 1"

|button| **Set2 Atoms**: Switches on assignment display and connections for atoms in "set 2"

|button| **All atoms**: Switches on assignment display and connections for all atom types 

Residues shown
~~~~~~~~~~~~~~


|selector| ***None***: Toggles particular kinds of residue on and off in the chart, still observing the above atom site selections; "off" residues are merely greyed out not removes

|button| **All residues**: Set all residue types, and any of the selected atom sites they contain, to be visible in the main chart

|button| **Invert Selection**: Make an inverse residue type selection, so that types that were not visible in the main chart now are, and those that were are now greyed out

Isotope Labelling
~~~~~~~~~~~~~~~~~


|pulldown| **Pattern**: If required, selects an isotope labelling scheme to use for colouring the atom site nodes

|float| **0.25**: Specifies the minimum fractional spin-active isotopic incorporation for an atom to be considered "labelled"

|pulldown| **Labelled Colour**: Selects which colour is use to display the atom site nodes in the main chart if they are unlabelled, according to the stated settings

|pulldown| **Isotope**: Selects which kind of nuclear isotope atom site colours are derived from using the selected scheme; typically 13C for checking C-C connections

|check| **Colour Gradient**: Whether, for labelled atom sites, to use a colour gradient with various hues to show isotopic incorporation, or otherwise only two colours for labelled & unlabelled

|pulldown| **Unlabelled Colour**: Selects which colour is use to display the atom site nodes in the main chart if they are isotopically labelled, according to the stated settings

