X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpaematrices.html;h=2f00e19f047da6d3f3509f907bdccf6c6e39e6cc;hb=b72ed01b68a8572022f912687db5be60b53c15cf;hp=8d180ee9780443022c9929477ccc7638ff9565b6;hpb=95443a95c1282c050fe1f28a4ddcaf3f0f75dfb4;p=jalview.git diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html index 8d180ee..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 shown in Jalview
-
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.

@@ -82,7 +94,92 @@ 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. +

+

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

+ +

+ Clustering PAE Matrices +

+

PAE matrices are useful for identifying regions of 3D structure + predictions that are likely to be positioned in space in the same or + similar way as shown in the predicted structure data. Regions of low + PAE often correlate with high alphafold reliability (PLDDT) scores, + but also complement them since they highlight well-folded regions such + as domains, and how well those regions have been predicted to be + positioned relative to eachother, which is important when evaluating + whether domain-domain interactions or other contacts can be trusted.

+

To make it more easy to identify regions of low PAE, Jalview can + cluster the PAE matrix, allowing columns of the matrix to be grouped + according to their similarity, using an Average Distance (UPGMA) tree + algorithm and the sum of differences between each column's PAE values.

+

+ distij = ∥ pi-pj + ∥ +

+

+ To create a PAE matrix tree, right click on a PAE annotation's label + to open the annotation popup menu, and select Cluster + Matrix. Once the calculation has finished, a tree viewer will open, + and columns of the matrix are then partitioned into groups such that + the third left-most node from the root is placed in its own group. + Colours are randomly assigned to each group, and by default these will + also be overlaid on the matrix annotation row. +

+

+

+ PAE matrices and Jalview Projects +

+

Any PAE matrices imported to Jalview are saved along side any + trees and clustering defined on them in Jalview Projects.

Support for visualision and analysis of predicted alignment error matrices was added in Jalview 2.11.3.