X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=3529cae8f9159e0691061cdbfeddbef0b2eee416;hb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;hp=66dbabd5705044b66a2a328b516e869cda69dfe2;hpb=cb56d532a3b7cc50d724b0761cc7c49ed2d081cd;p=jalview.git diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index 66dbabd..3529cae 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -1,7 +1,7 @@ By default, -points are only associated with the alignment view from which the PCA -was calculated, but this may be changed via the View→Associate -Nodes sub-menu.

-

Initially, the display shows the first three components of the -similarity space, but any eigenvector can be used by changing the -selected dimension for the x, y, or z axis through each ones menu -located below the 3d display. The Reset button will reset axis and rotation settings to their defaults.

-

-

-The output of points and transformed point coordinates was added to the Jalview desktop in v2.7. -The Reset button and Change Parameters menu were added in Jalview 2.8. -Support for PAM250 based PCA was added in Jalview 2.8.1. +left-clicking and dragging the mouse over the display. --> + By default, points are only associated with the alignment view from + which the PCA was calculated, but this may be changed via the View→Associate + Nodes sub-menu. +

+

+ Initially, the display shows the first three components of the + similarity space, but any eigenvector can be used by changing the + selected dimension for the x, y, or z axis through each ones menu + located below the 3d display. The Reset + button will reset axis and rotation settings to their defaults. +

+

+

+ The output of points and transformed point coordinates was + added to the Jalview desktop in v2.7. The Reset button + and Change Parameters menu were added in Jalview 2.8. Support + for PAM250 based PCA was added in Jalview 2.8.1. +

+

+ Reproducing PCA calculations performed with older + Jalview releases Jalview 2.10.2 included a revised PCA + implementation which treated Gaps and non-standard residues in the + same way as a matrix produced with the method described in the paper + by G. Casari, C. Sander and A. Valencia. Structural Biology volume + 2, no. 2, February 1995 (pubmed) + 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: + 

+    jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+    jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
+
+ 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). +