X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=3529cae8f9159e0691061cdbfeddbef0b2eee416;hb=54cbe6eeaf683e042246c657716514d80e561a9c;hp=0104078be6e66707cb67fe623f80be11858d150f;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 0104078..3529cae 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -60,15 +60,15 @@
     <em>Calculating PCAs for aligned sequences</em><br />Jalview can
     perform PCA analysis on both proteins and nucleotide sequence
     alignments. In both cases, components are generated by an
-    eigenvector decomposition of the matrix formed from the sum of
-    substitution matrix scores at each aligned position between each
-    pair of sequences - computed with one of the available score
-    matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
+    eigenvector decomposition of the matrix formed from pairwise similarity
+    scores between each pair of sequences. The similarity score model is 
+    selected on the <a href="calculations.html">calculations dialog</a>, and
+    may use one of the available score matrices, such as 
+    <a href="scorematrices.html#blosum62">BLOSUM62</a>,
     <a href="scorematrices.html#pam250">PAM250</a>, or the <a
       href="scorematrices.html#simplenucleotide">simple single
-      nucleotide substitution matrix</a>. The options available for
-    calculation are given in the <strong><em>Change
-        Parameters</em></strong> menu.
+      nucleotide substitution matrix</a>, or by sequence percentage identity,
+      or sequence feature similarity. 
   </p>
   <img src="pcaviewer.gif">
   <p>
@@ -78,8 +78,10 @@
     within the similarity space, as points in a rotateable 3D
     scatterplot. The colour of each sequence point is the same as the
     sequence group colours, white if no colour has been defined for the
-    sequence, and green if the sequence is part of a the currently
-    selected group.</p>
+    sequence, and grey if the sequence is part of the currently selected
+    group. The viewer also employs depth cueing, so points appear darker
+    the farther away they are, and become brighter as they are rotated
+    towards the front of the view.</p>
   <p>
     The 3d view can be rotated by dragging the mouse with the <strong>left
       mouse button</strong> pressed. The view can also be zoomed in and out with