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="loadpdbfromfile">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: 496px; height: 482px;"><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>