=====================================
Resonance : Reference Chemical Shifts
=====================================


.. |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


**Graphs and Charts of Database Chemical Shift Data**

This popup window presents the user with the distributions of known chemical
shift values, for various kinds of atom, as they appear in the BioMagResBank
or re-referenced RefDB databases. This information is useful when attempting
to determine the type of a residue from its NMR spectra, for example when
performing protein sequence assignment.

The popup is divided into two tabs for two different kinds of graphical
display. The first "1D graphs" tab shows the distributions of chemical shift
value for either hydrogens or other "heavy" atoms within a given kind of
residue. The buttons that carry atom names above the main graph can be toggled
two switch the display for different kinds of atom on or off.

The second "Amino Acid CA CB" tab is a special display to assist in the
assignment of protein sequences when using triple-resonance experiments
like HNCA/CB. Data for all of the common amino acids is displayed, but
only for the alpha and beta carbons.

**Caveats & Tips**

Two dimensional correlations, e.g. between a 1H resonance and a covalently
bound 13C will be added to Analysis in the future.

DNA and RNA chemical shift distributions is not present in the RefDB data, but
are present in the BMRB data; to view the BMRB data change the pulldown menu
at the top-right.

Some of the atom types have a second, minor chemical shift distribution, far
from the main peak, that is erroneous (this data is still present in the
source databases). An example of this is for the NE atom of the amino acid
arginine at around 115 ppm, which in this instance is probably caused by peaks
being assigned in HSQC spectra in the normal backbone amide ppm range when the
NE peak is really an aliased harmonic and should be a spectrum width away,
nearer 85 ppm.

Distributions that are notably jagged, due to lack of data for a given atom
type should naturally not be relied upon to any great degree.



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

|pulldown| **Source Database**: Whether to use chemical shift data from the BMRB (unfiltered) or RefDB sets

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

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

|button| **Close**: Close popup

1D Graphs
=========

Simple graphs of how chemical shift values are distributed for a given atom type

|pulldown| **Molecule Type**: Which of the common bio-polymer types to show data for

|pulldown| **Residue Code**: Which residue code to show chemical shift distributions for

|pulldown| **Atom Type**: Whether to show distributions for hydrogen atoms or other atoms

|selector| ***None***: The selection of atom name to display distributions for



Scrollbar: : 

Amino Acid CA CB
================

Density plots of alpha a & beta carbon shift distributions for common amnio acids


Scrollbar: : 

