X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FabovePID.html;h=8adacc9ab34d32083239fde7c76fa32525cc56a4;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=7c03cfabbab5992a09cdb48ef153b0edfb524974;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html index 7c03cfa..8adacc9 100755 --- a/help/html/colourSchemes/abovePID.html +++ b/help/html/colourSchemes/abovePID.html @@ -1,30 +1,44 @@ +
+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.
++ 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 at least a certain + percentage of the time. For instance, selecting the threshold to be + 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.