X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwcolour.html;h=9a96595b9d95f1cc7d15ca6a2bd6e5cb7b79f519;hb=a435a8668f8df568d3bdcf4e286210b69c18920c;hp=2c90bf9f289b2539f527d8ffa826d7ba54893641;hpb=96b6991703b70a1bbb0491f9946d397c9fcf5a38;p=jalview.git
diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html
index 2c90bf9..9a96595 100755
--- a/help/html/menus/alwcolour.html
+++ b/help/html/menus/alwcolour.html
@@ -1,43 +1,81 @@
-Alignment Window Menus
+
+
+Alignment Window Menus
+
-Alignment Window Colour Menu
+
+ Alignment Window Colour Menu
+
- Apply Colour To All Groups
- If this is selected, any changes made to the background colour
- will be applied to all currently defined groups.
-
- - Colour Text...
- Opens the Colour Text dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.
-
- - Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage
- Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
- Turn Propensity, Buried Index, Nucleotide, User Defined
- See colours for
- a description of all colour schemes.
+ If this is selected, any changes made to the background
+ colour will be applied to all currently defined groups.
+
+ - Colour
+ Text ...
Opens the Colour Text dialog box to
+ set a different text colour for light and dark background, and
+ the intensity threshold for transition between them.
+ - Colour Scheme options: None, ClustalX,
+ Blosum62 Score, Percentage Identity, Zappo, Taylor,
+ Hydrophobicity, Helix Propensity, Strand Propensity, Turn
+ Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+ Defined
+ See colours for
+ a description of all colour schemes.
+
+ - Sequence ID
Shades
+ sequences using their Sequence ID colour. Useful when performing
+ tree
+ based subfamily analysis.
+
- By Conservation
- See Colouring
- by Conservation.
-
+ See Colouring
+ by Conservation.
+
- Modify Conservation Threshold
- Use this to display the conservation threshold slider window.
- Useful if the window has been closed, or if the 'by conservation' option
- appears to be doing nothing!
-
+ Use this to display the conservation threshold slider
+ window. Useful if the window has been closed, or if the 'by
+ conservation' option appears to be doing nothing!
- Above Identity Threshold
- See Above Percentage
- Identity.
-
+ See Above
+ Percentage Identity.
+
- Modify Identity Threshold
- Use this to set the threshold value for colouring above Identity.
- Useful if the window has been closed.
-
- - By Annotation
- Colours the alignment on a per-column value from a specified annotation.
- See Annotation Colouring.
-
+ Use this to set the threshold value for colouring above
+ Identity. Useful if the window has been closed.
+
+ - By Annotation
Colours
+ the alignment on a per-column value from a specified annotation.
+ See Annotation
+ Colouring.
+
+ - By RNA Helices
Colours
+ the helices of an RNA alignment loaded from a Stockholm file.
+ See RNA
+ Helices Colouring.
+