X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Findex.html;h=51d0738325bbfdcf469f8cb095aff8165a3abe42;hb=624799db675c98a99302361c336a2cc2db3c5010;hp=450e1aae0921a13ffad9a38b7312ea7f59fbb1bb;hpb=e5cbd35e13f46ae1d59a08b0af1086677418141d;p=jalview.git diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html index 450e1aa..51d0738 100755 --- a/help/html/colourSchemes/index.html +++ b/help/html/colourSchemes/index.html @@ -1,7 +1,7 @@ - C - G - T - U - I - X - R - Y - N - W - S - M - K - B - H - D - V - - - Nucleotide - - - - - - - - - - - - - - - - - - - - - Purine/Pyrimidine - - - - - - - - - - - - - - - - - - - - - - - +

+ Colour schemes +

+

Jalview allows the user to set a colour scheme for the + whole alignment view or for each group defined on regions within it.

+

To change the colour for a view, simply select a new colour scheme from + the "Colour" menu.

+

To change the colour of a group, right click on any residue + within a group and use the popup menu to define the group colour.

+

At the top of the "Colour" menu you'll see a tick box + "Apply Colour to all groups". This is ticked by + default so that a chosen colour scheme will be applied to all + existing groups. If you wish to maintain the colour scheme for + defined groups, make sure you deselect this option before selecting + a new scheme in the Colour menu.

+

+ The "Colour→Colour Text..." + entry opens a dialog box to set a different text colour for light + and dark background, and the intensity threshold for transition + between them. +

+

The default colour schemes are summarised in the table below: +

+

 

+

+ Protein Colour Schemes +

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ARNDCQEGHILKMFPSTWYVBXZ
Clustal
Zappo
Taylor
Hydrophobicity
Helix Propensity
Strand Propensity
Turn Propensity
Buried Index
+
+

 

+

+ Nucleotide Colour Schemes +

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ACGTUIXRYNWSMKBHDV
Nucleotide
Purine/Pyrimidine
+
-
-

 

+ +