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=f0ae1616b89741f2e10e1510ba5c0b40a3b0f3a7;hb=e086b0c30bee5fe084186c65ef1ded42c58560f9;hp=51d0738325bbfdcf469f8cb095aff8165a3abe42;hpb=e51f922b88b1f316e27cf4c19eef437ff592d74d;p=jalview.git diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html index 51d0738..f0ae161 100755 --- a/help/help/html/colourSchemes/index.html +++ b/help/help/html/colourSchemes/index.html @@ -49,355 +49,384 @@ td { a new scheme in the Colour menu.

The "Colour→Colour Text..." + href="textcolour.html">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
-
+

+ Dynamic colour schemes +

+

+ Alignments and groups may be coloured according to associated sequence and alignment + annotation. Any applied colour schemes (such as those shown in the + table below) can also be shaded by + amino acid physico-chemical property conservation to reveal patterns + of variation, or applied selectively to Above + Identity Threshold. +

+

+ Alignments and groups can also be shaded according to percentage + abundance of aligned residues (using Percentage + Identity), and for protein alignments, the BLOSUM + 62 Score and ClustalX shading schemes + highlight amino acid conservation. +

+

+ The Sequence ID colour scheme shades sequences with + the same colour assigned to their Sequence ID. Colours are assigned + when groups are created by partitioning + a tree or subdividing the alignment by sequence with Select→Make + Groups For Selection. +

+

+ Amino acid and Nucleotide based colour schemes +

The built-in colour schemes based on amino acid and nucleotide symbols 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
+
-
-

 

+
+