From: James Procter Date: Thu, 5 Oct 2023 07:04:49 +0000 (+0100) Subject: JAL-4090 JAL-3858 paedocs X-Git-Tag: Release_2_11_4_0~138^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=426894b9cd99748534a5c684e9dc1d0bab90a660;p=jalview.git JAL-4090 JAL-3858 paedocs --- diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html index 43f059f..2f00e19 100644 --- a/help/help/html/features/paematrices.html +++ b/help/help/html/features/paematrices.html @@ -43,9 +43,22 @@ href="https://alphafold.ebi.ac.uk/entry/O04090">O04090 3D model at EBI-AlphaFoldDB).

-
-
Alignment of EPAS1 homologs from Human, Rat and Cow
with predicted alignment error tracks
-
Predicted Alignment Error Matrix
from https://alphafold.ebi.ac.uk/entry/Q99814
+
+
+ +
+ Alignment of EPAS1 homologs from Human, Rat and Cow
with + predicted alignment error shown for Human +
+
+
+ +
+ Predicted Alignment Error for Human EPAS1
from https://alphafold.ebi.ac.uk/entry/Q99814 +
+

Importing PAE Matrices @@ -56,10 +69,9 @@ href="../features/structurechooser.html">Jalview's structure chooser GUI. If you have produced your own models and accompanying PAE matrices using a pipeline such as ColabFold, then you can load - them both together via the - Load PDB - File dropdown menu in the 3D structure chooser, providing it is - in a + them both together via the Load PDB + File dropdown menu in the 3D structure chooser, providing it is in a supported PAE format.

@@ -81,23 +93,93 @@ Reference Annotation' entry in the Sequence ID submenu, or select all sequences and locate the option in the Selection submenu. You can do this in any alignment window (or view) where a sequence with - associated PAE data appears.

-

Adjusting the height of PAE matrix annotations

-

PAE annotations behave in the same way as Jalview's line graph and histogram tracks. Click+dragging up and down with the left (select) mouse button held down will increase or decrease the height of the annotation. You can also hold down SHIFT whilst doing this to adjust the height of all PAE rows at once. -

+ associated PAE data appears.

- PAE matrix annotation rows behave like any other sequence associated annotation, with the following additional features: + Adjusting the height of PAE matrix annotations

+

+ PAE annotations behave in the same way as Jalview's line graph and + histogram tracks. Click+dragging up and down with the left (select) + mouse button held down will increase or decrease the height of the + annotation. You can also hold down SHIFT + whilst doing this to adjust the height of all PAE rows at once. +

+

PAE matrix annotation rows behave like any other sequence + associated annotation, with the following additional features: