Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews

[jalview.git] / help / help / html / features / structurechooser.html

diff --git a/help/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html
index 2c77049..f91b1dd 100644 (file)
--- 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>