JAL-2418 JAL-2398 JAL-2397 simpler documentation for reinstating legacy behaviour

[jalview.git] / help / html / calculations / pca.html

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 14bb9ee..0104078 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -142,16 +142,14 @@ left-clicking and dragging the mouse over the display. -->
     and implemented at the SeqSpace server at the EBI. To reproduce
     calculations performed with earlier Jalview releases it is necessary
     to execute the following Groovy script:
-  
   <pre>
     jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+    jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
     </pre>
-  Additionally, for PCAs performed with older versions of Jalview and
-  the Blosum62 matrix, it is also necessary to import the legacy
-  BLOSUM62 score matrix (which is asymmetric for mutations between C to
-  R) which can be downloaded at
-  http://www.jalview.org/examples/legacyBlosum62.scm
+  This script enables the legacy PCA mode where gaps were treated as
+  'X', and to modify the BLOSUM62 matrix so it is asymmetric for
+  mutations between C to R (this was a typo in the original Jalview
+  BLOSUM62 matrix which was fixed in 2.10.2).
   </p>
-
 </body>
 </html>