From 985903ad810d9ef6ba0d09ff2b29d24e22c0708d Mon Sep 17 00:00:00 2001 From: James Procter Date: Tue, 26 Sep 2023 11:59:56 +0100 Subject: [PATCH] JAL-3858 JAL-4090 pae matrix docs. WIP --- help/help/html/features/paematrices.html | 44 ++++++++++++++++++------------ 1 file changed, 27 insertions(+), 17 deletions(-) diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html index e883bdb..d229251 100644 --- a/help/help/html/features/paematrices.html +++ b/help/help/html/features/paematrices.html @@ -29,11 +29,20 @@ Jalview

-

Predicted Alignment Error (PAE) matrices are produced by deep-learning - based 3D-structure prediction pipelines such as AlphaFold. They reflect how reliably two parts of a model have been positioned in space, by giving for each residue the likely error (in Angstroms) between the modelled position and the pair of residues' real relative position.

-

- Jalview visualises PAE matrices as an alignment annotation track, shaded from dark green to white, as used on the EBI-AlphaFold website (see ) -

+

Predicted Alignment Error (PAE) matrices are produced by + deep-learning based 3D-structure prediction pipelines such as + AlphaFold. They reflect how reliably two parts of a model have been + positioned in space, by giving for each residue the likely error (in + Ångstroms) between that residue and every other modelled + position the pair of residues' real relative position, if the model + and real 3D structure were superimposed at that residue.

+

+ Jalview visualises PAE matrices as an alignment annotation track, + shaded from dark green to white, similar to the encoding used on the + EBI-AlphaFold website (see O04090 3D model + at EBI-AlphaFoldDB). +

Importing PAE Matrices

@@ -55,22 +64,23 @@ annotated with PAE matrices and PLDDT scores.

- See Working with PAE - Matrices for information on how they are visualised and analysed in - Jalview. -

+ Showing PAE Matrix Annotations

- An additional Predicted Alignment Error file can also be - provided when importing 3D structure data. Jalview supports import of - PAE Matrices provided as AlphaFold - format JSON files - which are also produced by ColabFold. See Working with PAE Matrices for details on - what Jalview allows you to do with associated PAE matrix data. + When viewing 3D structures from the EBI-AlphaFold database or local 3D + structures with an associated PAE file, the PAE is imported as Reference + Annotation, which is not always automatically added to the alignment + view.

+

To show the PAE, right click the sequence and locate the 'Add + 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.

+

- The Structure Chooser interface was introduced in Jalview - 2.9. + Support for visualision and analysis of predicted alignment + error matrices was added in Jalview 2.11.3.

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