Working with PAE Matrices in Jalview

From: James Procter Date: Thu, 21 Sep 2023 16:17:01 +0000 (+0100) Subject: JAL-3858 JAL-3855 documentation for import and display PAE from alphafold and JSON... X-Git-Tag: Release_2_11_3_0~8^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8ad61a82f512a4f52dc8054f2ea4767e25e34d70;hp=d719653564e19ad9c3943f21971c13dae6c6bdf6;p=jalview.git JAL-3858 JAL-3855 documentation for import and display PAE from alphafold and JSON format flat files for Import 3D structure from file --- diff --git a/help/help/html/features/local-pdb-import.png b/help/help/html/features/local-pdb-import.png new file mode 100644 index 0000000..814ce6e Binary files /dev/null and b/help/help/html/features/local-pdb-import.png differ diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html new file mode 100644 index 0000000..cebc16b --- /dev/null +++ b/help/help/html/features/paematrices.html @@ -0,0 +1,65 @@ + + + +Working with PAE Matrices in Jalview + + + +

+ Working with Predicted Alignment Error Matrices in + Jalview +

+ +

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

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

+ 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. +

+ 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. +

+ The Structure Chooser interface was introduced in Jalview + 2.9. +

+ + diff --git a/help/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html index 2c77049..bfd8baa 100644 --- a/help/help/html/features/structurechooser.html +++ b/help/help/html/features/structurechooser.html @@ -176,21 +176,47 @@ style="width: 464px; height: 173px;">
Manual selection/association of PDB files with Sequences

To manually associate PDB files with a sequence, select 'From - File', or 'Enter PDB Id' from the drop-down menu: -

From File - allows you to load a PDB file - from the local machine or network and associate it with the - selected sequence. PDB files associated in this way will also be - saved in the Jalview Archive file.
Enter PDB Id - allows you specify a PDB ID - for your sequence. The PDB Rest API, provided by EMBL-EBI, is used - to validate and fetch structure data.

- -

- The Structure Chooser interface was introduced in Jalview - 2.9. -

+ Manual Association of PDBe accessions with sequences +

If for some reason the PDBe and 3D beacons search fail to + automatically the PDB structure or model you wish to import, you can + select 'Enter PDB Id' from the drop-down menu to manually specify PDB + identifiers for one or more selected sequences. The PDB Rest API, + provided by EMBL-EBI, is used to validate accessions exist, and fetch + structure data.

+ Import structure models + and metadata from file +

+ Selecting the From File option from the drop down + menu allows 3D structure data to be imported from your own computer. + PDB or mmCIF files associated in this way are also saved in Jalview Projects.

+ The 'From File' dialog provides a drop down menu which allows you to + specify how the Temperature Factor metadata for each residue in the 3D + structure data file is interpreted: + +

Default - Jalview will try to automatically determine whether + to show as 'Temperature Factor', 'AlphaFold Reliability' or 'Model + Quality'
PLDDT - Model has PLDDT scores in the temperature factor + column.

+ The Structure Chooser interface was introduced in Jalview + 2.9. +

diff --git a/help/help/html/io/paematrixformat.html b/help/help/html/io/paematrixformat.html new file mode 100644 index 0000000..9cf57d9 --- /dev/null +++ b/help/help/html/io/paematrixformat.html @@ -0,0 +1,71 @@ + + + +Supported Formats for Predicted Alignment Error Matrices + + + +

+ Supported Formats for Predicted Alignment Error + Matrices +

+ Predicted Alignment Error matrices are square matrices produced as + part of deep-learning based 3D-structure prediction pipelines such as + AlphaFold. They can be imported via Jalview's structure + chooser GUI and the Command + Line Interface. See Working + with PAE Matrices for information on how they are visualised and + analysed in Jalview. +

+ Supported Formats +

Jalview supports import of PAE matrix data as provided by the + EBI-AlphaFold database. This resource provides PAE matrices as a JSON + files structured in one of the following ways:

+	# Version 1 format PAE file - deprecated 28th July 2022
+	{
+		residue1:[1,1,... total number of residues]
+		residue2:[1,2,... total number of residues]
+		distance:[0.1,0.3,... list of PAE matrix elements as doubles]
+	}
+

+  	# Version 2 format PAE file - see https://alphafold.ebi.ac.uk/faq
+  	{
+  		max_predicted_alignment_error: 4.0, # may also be max_pae
+  		predicted_alignment_error: [[1,2,0,0,3,...],...] # may also be pae
+  	}
+

+ Variants of the version 2 format include using 'pae' instead of + 'predicted_alignment_error' in the names of keys. Jalview copes both.
+ Once imported, Jalview stores PAE matrices as float arrays along with + any associated tree and partition set resultant from clustering the + matrix.

PAE Matrix import support was added in Jalview 2.11.3 + +

+ +