X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpaematrices.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fpaematrices.html;h=cebc16ba152d7d7f0a86d31eff5f49c73d509da3;hb=8ad61a82f512a4f52dc8054f2ea4767e25e34d70;hp=0000000000000000000000000000000000000000;hpb=d719653564e19ad9c3943f21971c13dae6c6bdf6;p=jalview.git 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.

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

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+ 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. +

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+ 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. +

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

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