X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FabovePID.html;h=ad47daefbadf9677eb188e7eff47b6f7c7895e4a;hb=cd8f0eb5083ecbb73bde4b87c45e0d4286998ab9;hp=65e0e1957941df7696d05d98f35e3f980673c173;hpb=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html index 65e0e19..ad47dae 100755 --- a/help/html/colourSchemes/abovePID.html +++ b/help/html/colourSchemes/abovePID.html @@ -1,20 +1,45 @@ - -Above PID Colours - - - - -

Colouring above a percentage identity threshold

-

Selecting this option causes the colour scheme to be applied to only those - residues that occur in that column more than a certain percentage of the time. - For instance selecting the threshold to be 100 will only colour those columns - with 100 % identity. This threshold option can be applied to the Zappo, Taylor, - Hydrophobicity and User colour schemes.

- - + + + +Above PID Colours + + + + +

+ Colouring above a percentage identity threshold +

+

Selecting this option causes the colour scheme to be applied to + only those residues that occur in that column more than a certain + percentage of the time. For instance, selecting the threshold to be + 100 will only colour those columns with 100% identity.

+

To be coloured, a residue must match the consensus (most commonly occurring) residue for the column (or joint equal consensus).

+

The percentage calculation may include or exclude gaps in the column, depending on the option selected for the consensus calculation.

+

With a threshold of 0, colouring is unchanged (including non-consensus residues).

+ +