From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 3 Oct 2023 06:57:40 +0000 (+0100)
Subject: Merge branch 'develop' into doc/JAL-4090_Release_2_11_3_0
X-Git-Tag: Release_2_11_3_0~5^2^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=88446805fceab891ff2f229415a4744851d09c13;hp=-c;p=jalview.git

Merge branch 'develop' into doc/JAL-4090_Release_2_11_3_0
---

88446805fceab891ff2f229415a4744851d09c13
diff --combined help/help/html/features/paematrices.html
index 66b0be6,8d180ee..43f059f
--- a/help/help/html/features/paematrices.html
+++ b/help/help/html/features/paematrices.html
@@@ -44,7 -44,7 +44,7 @@@
  		at EBI-AlphaFoldDB).
  	</p>
  	<div style="display:flex; flex-wrap:wrap;"align="center" width="100%">
 -	<figure><img src="../structures/epas1_annotdetail.png" height="300"/><figcaption>Alignment of EPAS1 homologs from Human, Rat and Cow, with predicted alignment error shown in Jalview</figcaption></figure>
 +	<figure><img src="../structures/epas1_annotdetail.png" height="300"/><figcaption>Alignment of EPAS1 homologs from Human, Rat and Cow<br/>with predicted alignment error tracks</figcaption></figure>
  	<figure><img src="../structures/epas1_pae_ebiaf.png" height="300"/><figcaption>Predicted Alignment Error Matrix<br/>from <a href="https://alphafold.ebi.ac.uk/entry/Q99814">https://alphafold.ebi.ac.uk/entry/Q99814</a></figcaption></figure>
  	</div>
  	<p>
@@@ -56,10 -56,11 +56,11 @@@
  			href="../features/structurechooser.html">Jalview's structure
  			chooser</a> 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 <a
- 			href="../features/structurechooser.html#loadpdbfile">Load PDB
- 			File</a> dropdown menu in the 3D structure chooser. in a <a
- 			href="../io/paematrixformat.html">supported PAE format</a>.
+ 		them both together via the
+ 		<a href="../features/structurechooser.html#loadpdbfile">Load PDB
+ 			File</a> dropdown menu in the 3D structure chooser, providing it is
+ 		in a
+ 		<a href="../io/paematrixformat.html">supported PAE format</a>.
  	</p>
  	<p>
  		The <a href="../features/clarguments-basic.html">Command Line
@@@ -80,23 -81,8 +81,23 @@@
  		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.</p>
 +	  associated PAE data appears.</p>
 +	<p><strong>Adjusting the height of PAE matrix annotations</strong></p>
 +	  <p>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 <strong><em>SHIFT</em></strong> whilst doing this to adjust the height of all PAE rows at once. 
 +	  </p>
 +	<p>
 +	  PAE matrix annotation rows behave like any other sequence associated annotation, with the following additional features:
 +	</p>
 +	<ul>
 +	  <li>The vertical axis of the PAE heatmap is mapped to positions on the linked 3D structure.
 +	    <ul><li>Moving the mouse over any part of the heatmap highlights the corresponding regions of the 3D structure the PAE data is associated with, in addition to a tooltip being displayed giving information on the range of values under the mouse.</li>
 +	      <li>Clicking to select positions in the matrix results in columns of the alignment corresponding to the row and columns selected in the matrix.</li>
 +	</ul>
  	<p></p>
 +	    <p><strong><a name="clustering">Clustering PAE Matrices</a></strong></p>
 +	    <p>
 +	      
 +	</p>
  	<p>
  		<em>Support for visualision and analysis of predicted alignment
  			error matrices was added in Jalview 2.11.3. </em>