X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Findex.html;h=01319b73db793e7b3da8c859a424b1e1016a4159;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=0257099ae6d75634d7cbad91c0e378618cb7ed87;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html index 0257099..01319b7 100755 --- a/help/html/colourSchemes/index.html +++ b/help/html/colourSchemes/index.html @@ -1,21 +1,24 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Colour Schemes -

Colour schemes

-

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

-

To change the background colour, simply select the colour 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 the tick box -"Apply Background 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 changing the background -colour.

-

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: -

-

 

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

 

+

+ Colour schemes +

+

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

+

To change the background colour, simply select the colour 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 the tick box + "Apply Background 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 changing + the background colour.

+

+ 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
+
+ + +
+