X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwcolour.html;h=2ad79d591cea6b658056894c280d5dfe08843d8f;hb=c2214808f64b811a25cec10399dcff38db0c592c;hp=2c90bf9f289b2539f527d8ffa826d7ba54893641;hpb=96b6991703b70a1bbb0491f9946d397c9fcf5a38;p=jalview.git diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html index 2c90bf9..2ad79d5 100755 --- a/help/html/menus/alwcolour.html +++ b/help/html/menus/alwcolour.html @@ -1,4 +1,24 @@ + Alignment Window Menus @@ -8,12 +28,13 @@ If this is selected, any changes made to the background colour will be applied to all currently defined groups.
 -
  • Colour Text...
    +
  • 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
    + Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined
     See colours for a description of all colour schemes.
    • @@ -38,6 +59,11 @@ 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.
    +