=======================
Molecule : Atom Browser
=======================


.. |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


**Select Atoms and Residues for Assignment**

This popup window allows the user to view and select specific atom, atom set
and residue entities from any of the molecular systems within the CCPN
project. Most importantly this allow the user to perform resonance assignment,
of the signal phenomena observed in NMR spectra, to particular atomic groups,
thus labelling the origin of a resonance. In a similar manner, spin systems
(groups of resonances from the same residue) may be linked to residues. In
Analysis such atom and residue assignment may be performed in a specific way,
i.e. choosing a particular atom in a particular residue within the sequence.
However, this system also allows the user to select atoms and  residues in
order to specify the type of a resonance or spin system; to say what kind of
atom or residue a resonance or spin system relates to without actually
specifying which position in the molecular sequence. This type-only
information is useful to reflect the current state of knowledge, particularly
during early stages of assignment, without having to make notes outside of the
CCPN system.

This system has a second important function, to show the user the current
assignment state for the atoms of the selected chemical element types,
molecular chain (and bearing in mind any shift list) selection. The cells
within the table will show a darker colour if they carry a resonance
assignment (irrespective of whether the resonance is associated with peaks)
and thus the user can quickly get a visual appreciation of the parts of the
molecular chain that have been assigned and those that have yet to be assigned

**Atom Table**

In order to use this system the user must ensure that the various options have
been chosen appropriate to what they wish to view. Generally in the first
"Atom Table" tab the user selects which molecular chain in the upper left
pulldown men and click the "Elements" buttons to specify which kinds of atom
will be visible at this time. Naturally the selection of chemical elements
will reflect the kind of operation or assignment that is being performed at
the  time. Thus for example if the user is assigning a 15N HSQC NOESY
experiment which shows only 15N and 1H resonances then only the [H] and [N]
chemical element buttons need to be toggled on. If the user wants to reduce
clutter and only look at a particular type of residue (amino acid, nucleotide,
sugar) then the "Residue" pulldown can be used to display only a subset of
the sequence. The adjacent "Nucleotides" option is only relevant for nucleic
acids like DNA & RNA, and allow the user the option of showing each residue on
a single line (long row), or have the sugar phosphate and aromatic bas
components displayed independently on separate lines; minimising clutter and
the need to scroll.

There are a few functions at the bottom of the first tab that control
assignment and link to other kinds of data entity in the CCPN project. The
[Show ...] buttons allow the user to get a separate table of either the
spectrum peaks or resonance phenomena that have been associated with the atoms
or resonances that have been selected in the table above. Specifically the
`Selected Peaks`_ and `Selected Resonances`_ popups are opened. This is useful
to navigate from the molecule based information display into the spectrum
display and to understand the links throughout the project. The [Remove Atom
Assignments] button does as the name suggests and disconnects any resonances
assigned to the selected atoms from those atoms. This merely removes the
specific atom information for those resonances, it does not affect the linking
of the resonances to any peaks. Lastly the [Set Ring Flip Equivalency] button
is used on the selected residue for the rare occasions that aromatic rings (in
residues like Phe & Tyr) display two distinct resonances for atoms that in
most circumstances are indistinguishable in NMR spectra, because they are in
very rapid exchange due to rotation of the aromatic ring around an axis of
symmetry. In essence this makes Phe & Thr HD*, CD, HE* and CE separate into
HD1, HD2, CD1, CD2, HE1, HE2, CE1 & CE2 selections. This operation is
reversible but will naturally loose fidelity of peak assignments if a peak is
assigned to only one side of the ring.

**Options**

The second tab gives the user further control over how atom information is
displayed in the main table. The upper "Prochirals" section allows the choice
of how to display stereochemical information for atom sets that are often  not
distinguishable in stereospecific way in NMR spectra. For example a Ser residue
has both HB2 and HB3 atoms in its side chain, but these can prochiral atoms
cannot generally be distinguished from one another in NMR spectra. In such
circumstances it is commonplace to use non-stereospecific assignment labels
like "HBa" and "HBb" so that two different resonances, usually with different
chemical shifts, can be identified in NMR spectra, without needing to specify
any stereochemical information. In this example "HBa" and "HBb" resonance
assignments will both be linked to both HB2 and HB3, but this is done in a way
that is mutually exclusive; Analysis knows that one really only goes to HB2
and the other to HB3, whichever way round that may be. If the  user has
structural  information that allows a proper determination of which resonance
goes with which stereochemical location, then the "Stereospecific" option can be
set. This would make Ser HB2 and HB3 available as separate options to "HBa"
and "HBb" which come from the "Non-stereospecific" option. The "Ambiguous"
option is something of a remnant and is generally only used for situations
when the atoms in the stereo group have exactly the same chemical shift. For
Ser HB2 & HB3 this would provide the "HB*" option in the main table, however
this is really just a pseudonym; assigning to this actually assigns to both
the stereospecific HB2 and HB3 at the same time (not HBa, HBb).

The "Assignment Status" selection allows the number of atom options displayed
in the main table to be reduced by only showing specific cells based upon what
kind of assignment the underlying atoms have. For example the "unassigned"
option may be selected to view more easily what has yet to be assigned. The
"Shift List" pulldown controls which atom options are darkened, indicating
resonance assignments, based upon the experiments that those assignments are
made to and which set of conditions (and thus shift list) those assignments
relate. By default this option is set to "<Ignore>", meaning that all
resonance assignments are considered. Selecting a specific shift list will
reduce the indication of assignment to only those peaks that use that shift
list (via the experiment's connection).

The lower "Isotope Labelling" section is used if the user has any experiments
that were performed with selective spin-active isotope labelling, which would
reduce the complement of atom sites that were deemed to be visible in spectra
and thus available for assignment. Here, the user selects which type of isotope
labelling scheme was used, and what level of isotopic incorporation (between
0,0 and 1.0) must be present for an atom site to be visible.  Atom sites that
are not deemed to be visible will not be displayed in the  main sequence + atom
table.

**Tips and Caveats**

At some stage in the future it is planned that the Atom Table will become
(optionally) context sensitive to the kind of atoms that *ought* to be visible
in the specific spectrum being assigned at the time. For example if an HNCA
experiment is assigned then only the H, N & CA atom options cane be displayed.

.. _`Selected Peaks`: SelectedPeaksPopup.html
.. _`Selected Resonances`: BrowseResonancesPopup.html



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

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

|button| **Close**: Close popup

Atom Table
==========

*Documentation missing*

|pulldown| **Chain**: Select the molecular system & chain to show atoms for

|pulldown| **Residue**: Select the type of residue to display atoms for, defaults to all types

|pulldown| **Nucleotides**: Select how to display rows of base and sugar-phosphate atoms for DNA & RNA nucleotide residues

|selector| **Elements**: The selection of which chemical elements to display atoms for

===========  =================================
**Table 1**
----------------------------------------------
        *#*  Sequence number code 
  *Residue*  Residue type code 
===========  =================================



|button| **Set Ring Flip Equivalency**: Toggle whether the symmetric aromatic ring of selected residue
flips quickly on the NMR timescale

|button| **Remove Atom Assignments**: Remove all resonance assignments from the selected atoms

|button| **Show Peaks**: Show a table of all peaks assigned to the selected atoms

|button| **Show Resonances**: Show a table of all resonances assigned to the selected atoms

Options
=======

*Documentation missing*

Prochirals
~~~~~~~~~~


|check| **Non-Stereospecific**: Whether to show distinct but stereoscopically ambiguous assignment options.
For example you may not know if a Serine Hb is "Hb2" or "Hb3"

|check| **Stereospecific**: Whether to show stereospecific atom options (IUPAC system) like Serine Hb2 & Hb3

|check| **Ambiguous**: Whether to include multi-atom ambiguous options like Ser Hb*.
Methyl groups are not affected by this option unless the whole group is prochiral.

Assignment Status
~~~~~~~~~~~~~~~~~



|radio| **Any**: Show all atom options irrespective of assignments

|radio| **Assigned**: Show only atom options which are assigned to NMR resonances

|radio| **Unassigned**: Show only atom options which have no resonance assignments

|radio| **Tentative**: Show only atom options that carry tentative resonance assignments

|pulldown| **Shift List**: Select a specific shift list to determine an atoms assignment status or "<ignore>" to use any

Isotope Filtering
~~~~~~~~~~~~~~~~~


|pulldown| **Isotope Labelling**: Select which per-residue isotope labelling scheme/pattern to use

|float| **0.25**: Specify what proportion of atoms must be isotopically labelled (spin active) to be considered as assignable

