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Chart : Secondary Structure Chart
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.. |pulldown| image:: ../images/pulldown.png
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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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.. |ramp| image:: ../images/ramp.png
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.. |selector| image:: ../images/selector.png
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**Display NMR Evidence for Protein Secondary Structure**

This popup window is designed to collect together several kinds of NMR derived
information to give a visual representation of evidence to indicate the
regions of a protein chain with secondary structure, and what that structure
might be. This system collects data from several sources from through-space
(e.g. NOE) connectivity; from secondary chemical shifts; from a combined
chemical shift index; from 3J H-Ha scalar couplings.

The main chart lists the residue sequence of the selected chain (see
"Options"), the predicted secondary structure of the residues and various
types of evidence of the secondary structure. The "Sec Struc" column may be
set manually based on the contents of the table via the [Set ...] buttons at
the bottom, or automatically via a program like DANGLE_. In the table the
eight through-space connectivity columns (d_aN i,i+1 to da_N i,i+2) are always
displayed, but the other columns relating to chemical shift are optional and
may be toggled via the top buttons. The connectivity columns are filled with a
green colour if a given kind of connectivity is observed for a residue,
additionally for the first three of these there is an extra distinction of
strong (S) medium (M) and weak (W) categories. The name of a column indicates
what kind of connectivity is present, for example d_aN i,i+1 represents the
connection of an alpha position of one amino acid residue to the amide
position of a residue one position further along (C-terminal) in the chain.

The Delta-delta columns indicate secondary chemical shifts for Ca, Cb, C' and
Ha atoms; the difference from recorded chemical shift to (sequence adjusted)
random coil chemical shift. The random coil chemical shifts are calculated as
specified in Schwarzinger et  al. as detailed below. These secondary chemical
shifts are combined to give the CSI values (calculated according to the methods
in the papers listed below) indicating the secondary structure type; -1
indicates alpha-helix and +1 beta-strand. The last "3JHNHa" column lists any
recorded scalar couplings between the amide and alpha hydrogens of a residue.
These are indicative of the phi backbone angle, according to the Karplus
relationship. These coupling values may be extracted and analysed in more
detail using the Data Analysis : `3J H-Ha Coupling`_ system.

The "Chart" tab shows a graphical representation of the secondary structure
evidence data. This is the same data that is shown in the first table, it is
merely presented differently, on a compact graphical form that may be printed
out by making a PostScript file (right mouse menu). The order of the rows of
data in the chart is the same order as the columns of the evidence table. The
grey and white panels of the chart delineate the display into regions of ten
residues. The text font used in the chart and the number or residues that
are shown in a row, before the chart wraps back to start at the left again,
are governed by settings in the last "Options Tab".

The "Options" tab controls various aspects of how the data in the other tabs
is displayed. The "Chain" naturally selects the sequence to use and "Shift
List" is the source of the secondary chemical shift information. The "NOE
Intensity Classes" section allows the user to set two values which distinguish
between strong, medium and weak connection strength. Note that these values
represent a peak intensity relative to the average in the peak list containing
the connection. The lower table lists the peak lists that are used as sources
of through-space connectivity information. The use can toggle to consider or
reject particular peak lists by double clicking in the "Consider?" column. Any
changes to any of these settings will be reflected one the user selects one
of the first two tabs.

**Caveats & Tips**

The most accurate secondary structure prediction currently available in
CCPN comes from the embedded DANGLE_ program. Although DANGLE has a separate
graphical interface its secondary structure predictions, if committed, will be
visible in this system via the displayed secondary structure classification.

Regions of a polypeptide backbone with stable secondary structure will tend to
show more near-sequence ("short range") though-space connectivities than
unstructured, flexible  regions; commonly termini and loops. Naturally
alpha-helices will tend to show i to i+3 and i to i+4 connections, due to the
periodicity of the helix. Beta strand regions will often show i to i+2
connectivity by lack i to i+3 and i to i+4, given that stands are extended
conformations.

**References**

Secondary chemical shifts:

*Schwarzinger, S., Kroon, G. J. A., Foss, T. R., Chung, J., Wright, P. E., Dyson, H. J.
"Sequence-Dependent Correlation of Random Coil NMR Chemical Shifts",
J. Am. Chem. Soc. 123, 2970-2978 (2001)*

Chemical Shift Index

*Wishart DS, Sykes BD.
The 13C chemical-shift index: a simple method for the identification of protein
secondary structure using 13C chemical-shift data.
J Biomol NMR. 1994 Mar;4(2):171-80.*

*Wishart DS, Sykes BD, Richards FM.
The chemical shift index: a fast and simple method for the assignment of protein
secondary structure through NMR spectroscopy.
Biochemistry. 1992 Feb 18;31(6):1647-51.*

.. _DANGLE: DanglePopup.html
.. _`3J H-Ha Coupling`: CalcHnHaCouplingPopup.html


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

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

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

|button| **Close**: Close popup

Residue Data
============

A table of the evidence used to estimate the secondary structure type of residues

|selector| **Column Options**: Selects which of various secondary chemical shifts, chemical shift index or 3J H-Ha coupling data to display in the table and chart

============  ================================================================================================
**Table 1**
--------------------------------------------------------------------------------------------------------------
   *Residue*  The sequence number and residue type 
 *Sec Struc*  The stated secondary structure type for the residue 
*d_αN i,i+1*  Indicates residue that show an alpha(i) to amide(i+1) through-space/NOE connection 
*d_NN i,i+1*  Indicates residue that show an amide(i) to amide(i+1) through-space/NOE connection 
*d_βN i,i+1*  Indicates residue that show a beta(i) to amide(i+1) through-space/NOE connection 
*d_αN i,i+3*  Indicates residue that show an alpha(i) to amide(i+3) through-space/NOE connection 
*d_αβ i,i+3*  Indicates residue that show an alpha(i) to beta(i+3) through-space/NOE connection 
*d_αN i,i+4*  Indicates residue that show an alpha(i) to amide(i+4) through-space/NOE connectio 
*d_NN i,i+2*  Indicates residue that show an amide(i) to amide(i+2) through-space/NOE connection 
*d_αN i,i+2*  Indicates residue that show an alpha(i) to amide(i+2) through-space/NOE connection 
   *Δ δ13Cα*  Carbon alpha secondary chemical shift (difference to random coil value) 
   *Δ δ13Cβ*  Carbon beta secondary chemical shift (difference to random coil value) 
   *Δ δ13C'*  Backbone carbonyl carbon secondary chemical shift (difference to random coil value) 
    *Δ δ1Hα*  Hydrogen alpha secondary chemical shift (difference to random coil value) 
============  ================================================================================================



|button| **Set Alpha**: Set the secondary structure type for the selected residue to "Alpha"

|button| **Set Beta**: Set the secondary structure type for the selected residue to "Beta"

|button| **Set Coil**: Set the secondary structure type for the selected residue to "Coil"

|button| **Set Undef**: Set the secondary structure type for the selected residue to "Undef"

|button| **Read CSI File**: Read CSI information for the residue from a CSI output file

|button| **Make Chart**: Display the secondary structure evidence information as a graphical chart, which may then be saved as a PostScript file

Chart
=====

The secondary structure evidence information as a graphical chart, which may then be saved as a PostScript file



Options
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The various parameters that control the data display, including which peak lists and molecule chain to use

|pulldown| **Chain**: Selects which molecular chain to secondary structure evidence for

|pulldown| **Shift List**: Selects which shift list chemical shifts are derived from, for calculating deltas etc.

**Chart Font**: Sets the typeface to use in the main chart display

|pulldown| **Residue Wrap Width**: Sets how wide, in terms of number residues, the main chart is; will cause sequences to wrap back to the start

NOE Intensity classes
~~~~~~~~~~~~~~~~~~~~~


|float| **1.5**: The intensity value, relative to peak list average, that separates strong and medium NOE strength categories

|float| **0.3**: The intensity value, relative to peak list average, that separates weak and medium NOE strength categories

NOE peak lists
~~~~~~~~~~~~~~


===========  =======================================================================================================================================
**Table 2**
----------------------------------------------------------------------------------------------------------------------------------------------------
 *Spectrum*  The experiment:spectrum to which the through-space peak list belongs 
*Peak List*  The serial number of the through-space peak list within its spectrum 
*Consider?*  Whether the through-space peak list should be used to provide connectivity data for the secondary structure evidence table  *(Editable)*
===========  =======================================================================================================================================



