X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=f91b1dd58cc2038337f5df6b96964f89d50d1780;hb=b122ba188c2ffcbb302809bafc02058e355643ee;hp=2c77049d23515dd5cf07a0134281aaa58dfef65e;hpb=c902ed8d8708cf273963f4d08e2fd46d06280e0c;p=jalview.git

diff --git a/help/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html
index 2c77049..f91b1dd 100644
--- a/help/help/html/features/structurechooser.html
+++ b/help/help/html/features/structurechooser.html
@@ -176,21 +176,47 @@
       style="width: 464px; height: 173px;"> <br /> <strong>Manual
       selection/association of PDB files with Sequences</strong>
   </p>
-  <p>To manually associate PDB files with a sequence, select 'From
-    File', or 'Enter PDB Id' from the drop-down menu:
-  <ul>
-    <li><strong>From File</strong> - 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 <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
-    <li><strong>Enter PDB Id</strong> - 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.<br></li>
-  </ul>
-
-  <p>
-    <em>The Structure Chooser interface was introduced in Jalview
-      2.9. </em>
-  </p>
+	<p>
+		<strong>Manual Association of PDBe accessions with sequences</strong>
+	</p>
+	<p>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.</p>
+	<p>
+		<strong><a name="loadpdbfile">Import structure models
+				and metadata from file</a></strong>
+	</p>
+	<p>
+		Selecting the <strong>From File</strong> 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 <a
+			href="jalarchive.html">Jalview Projects</a>. <br /> <img
+			src="local-pdb-import.png" style="width: 330px; height: 321px;"><br />
+		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:
+	
+	<ul>
+		<li>Default - Jalview will try to automatically determine whether
+			to show as 'Temperature Factor', 'AlphaFold Reliability' or 'Model
+			Quality'</li>
+		<li>PLDDT - Model has PLDDT scores in the temperature factor
+			column.</li>
+	</ul>
+	<p>
+		An additional <em>Predicted Alignment Error</em> file can also be
+		provided when importing 3D structure data. Jalview supports import of
+		PAE Matrices provided as <a href="../io/paematrixformat.html">AlphaFold
+			format JSON files</a> - which are also produced by ColabFold. See <a
+			href="paematrices.html">Working with PAE Matrices</a> for details on
+		what Jalview allows you to do with associated PAE matrix data.
+	</p>
+	<p>
+		<em>The Structure Chooser interface was introduced in Jalview
+			2.9. </em>
+	</p>
 </body>
 </html>