X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpaematrices.html;h=2f00e19f047da6d3f3509f907bdccf6c6e39e6cc;hb=56ce5cb6fd0b54f831cf35859886cd69a7f522a3;hp=d22925179d438aa8442dd76b16c0d4cb1e6a66d0;hpb=985903ad810d9ef6ba0d09ff2b29d24e22c0708d;p=jalview.git diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html index d229251..2f00e19 100644 --- a/help/help/html/features/paematrices.html +++ b/help/help/html/features/paematrices.html @@ -43,6 +43,23 @@ href="https://alphafold.ebi.ac.uk/entry/O04090">O04090 3D model at EBI-AlphaFoldDB).
+Importing PAE Matrices
@@ -54,8 +71,8 @@ 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. in a supported PAE format. + File dropdown menu in the 3D structure chooser, providing it is in a + supported PAE format. - ++ 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:
+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.