X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FabovePID.html;h=8adacc9ab34d32083239fde7c76fa32525cc56a4;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=ad47daefbadf9677eb188e7eff47b6f7c7895e4a;hpb=0350dbbb4ab895c253162de8a108984826b9cb22;p=jalview.git diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html index ad47dae..8adacc9 100755 --- a/help/html/colourSchemes/abovePID.html +++ b/help/html/colourSchemes/abovePID.html @@ -35,11 +35,10 @@ td { 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 + only those residues that occur in that column at least 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).
+ 100 will only colour those columns with 100% identity, and selecting 50 will shade residues appearing in least 50% of the rows (or sequences) in each column.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).
+With a threshold of 0, colouring is unchanged.