<p>
Jalview can process PDB data associated with sequences to display
values extracted from the <em>Temperature Factor</em> column for
- corresponding sites, and secondary structure from DSSP or RNAView
- (as appropriate).
+ corresponding sites, and secondary structure from DSSP. For computationally determined structures, jalview will show
+ model quality data encoded in the temperature factor column as <em>AlphaFold Reliability</em> (PLDDT) or <em>Model
+ Quality</em> as appropriate.
</p>
<p>
<strong>Extracting data from PDB files<br /></strong>Annotation is
the <strong>Add Reference Annotation</strong> in the <strong>Selection</strong>
and <strong>Sequence ID</strong> sub-menus of the Sequence ID
Panel's popup menu.<br /> <em>Please note:</em>Protein structures
- are analysed <em>in situ</em>, but Jalview employs a web service to
- process RNA structures which can cause long delays if your internet
- connection is slow.
+ are analysed <em>in situ</em>.
</p>
<p>
The <a href="../menus/alwannotation.html"><em>Annotations</em>
alignment menu</a> provides settings useful for controlling the
- display of secondary structure annotation.
- </p>
+ display of sequence-associated annotation. To compare several tracks from different structures for one or more
+ sequences, use 'sort by label' - which will also display PDB and Chain IDs for secondary structure and temperature
+ factor/quality annotation tracks for easier identification.
+ </p>
<p>
<strong>Shading sequences by associated structure
annotation<br />
</strong>The annotation colouring dialog (opened by the <strong>Colour→By
- Annotation</strong> option) allows sequences with associated secondary
+ Annotation</strong> option) or by right-clicking a particular annotation tracks's label allows sequences with
+ associated secondary
structure data to be shaded according to secondary structure type.
Once the dialog is opened, select the <em>Per Sequence</em> option
and then choose <em>Secondary structure</em> from the dropdown menu.<br />When