From c10d8000dd752b76576db162dcd3d1e1925c0704 Mon Sep 17 00:00:00 2001 From: James Procter Date: Mon, 25 Sep 2023 17:55:38 +0100 Subject: [PATCH] JAL-3858 JAL-4090 PAE documentation.. --- help/help/html/features/paematrices.html | 35 ++++++++++++++++++++---------- 1 file changed, 23 insertions(+), 12 deletions(-) diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html index cebc16b..e883bdb 100644 --- a/help/help/html/features/paematrices.html +++ b/help/help/html/features/paematrices.html @@ -29,24 +29,35 @@ Jalview

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Predicted Alignment Error matrices are produced by deep-learning - based 3D-structure prediction pipelines such as AlphaFold.

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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.

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

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+ Importing PAE Matrices +

Jalview retrieves PAE matrices when importing predicted 3D structures from the EBI-AlphaFold database via Jalview's structure - chooser GUI. + 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. in a supported PAE format. +

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+ The Command Line + Interface also provides a options for importing PAE matrices along + side models, enabling the automated production of alignment figures + annotated with PAE matrices and PLDDT scores.

- If you have produced your own models using a pipeline such as - ColabFold, then you can load it via the 'Add PAE matrix file' button - in the Load - PDB File dropdown menu in the 3D structure chooser, providing it is - in a supported PAE format. , - or the Command Line - Interface. See Working - with PAE Matrices for information on how they are visualised and - analysed in Jalview. + See Working with PAE + Matrices for information on how they are visualised and analysed in + Jalview.

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