X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FcolourSchemes%2Findex.html;fp=help%2Fhelp%2Fhtml%2FcolourSchemes%2Findex.html;h=51d0738325bbfdcf469f8cb095aff8165a3abe42;hb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;hp=0000000000000000000000000000000000000000;hpb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;p=jalview.git diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html new file mode 100755 index 0000000..51d0738 --- /dev/null +++ b/help/help/html/colourSchemes/index.html @@ -0,0 +1,403 @@ + + + +Colour Schemes + + + +

+ 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
+
+ + +
+

 

+ +