Viewing AlphaFold Models in Jalview

  1. Launch Jalview. Open Jalview $\Rightarrow$ Preferences in the Jalview desktop window. In the preferences Structure tab, ensure the Temperature Factor option is enabled.

  2. Select Window $\Rightarrow$ Close All in the Jalview desktop menu.

  3. Select File $\Rightarrow$ Fetch Sequences… from the desktop menu. In the New Sequence Fetcher dialog box, select the Uniprot database from the —Select Database— drop-down menu. Enter the accession number O04886 and hit return. Select the O04886 entry and click OK.

  4. In the alignment window, select View $\Rightarrow$ Show Sequence Features and ensure that the show sequence features option is ticked.

  5. Select View $\Rightarrow$ Feature Settings. . . to open the Sequence Features Settings dialog box. Click the Optimise Order button. This re-orders the features based on the average length of the feature type.

  6. In the Show column, untick the check box for all features except the three called site, active site and binding site. Note the unticked features are no longer visible on the sequence.

  7. In the Colour column, change the colour of the visible features to more distinct colours using the Select Colour dialog box. Close the Sequence Feature Settings dialog box by clicking OK.

  8. To view the location of the coloured features, open the overview window by selecting View $\Rightarrow$ Overview Window in the alignment window. Reposition and resize the overview window. Use the red box to scroll across the sequence.

  9. To view the entire sequence in the alignment window, select Format $\Rightarrow$ Wrap and scroll to the top of the sequence. Hide the annotation rows if present, by going to Annotations ⇒ Show annotations and deselecting the show option.

  10. Place the mouse cursor on one of the coloured amino acid residues in the sequence and note the information in the tooltip. Extra information is also present in the status bar in the lower left-hand corner of the alignment window.

  11. Right-click on the sequence ID name PME1_CITSI and select 3D Structure Data… in the context menu. In the Structure Chooser dialog box that opens select the AlphaFold model for PME1_CITSI with ID AF-O04886-F1 from the list. Click Open new structure view with button.

  12. Resnum feature has been loaded and the structure may now be coloured green. The colouring can be removed by opening the Sequence Features Settings dialog box and unticking it in the show column.

  13. Right-click on the sequence ID name PME1_CITSI and select Selection $\Rightarrow$ Add reference annotations in the context menu. The Alphafold Reliability scores appears as an annotation row. To view the annotation rows select Annotations ⇒ Show annotations.

  14. The Alphafold Reliability score can be used to colour the model by selecting Colour $\Rightarrow$ By Annotation. In the Colour by Annotation dialog box that opens, select AlphaFold Reliability and Above Threshold in the drop-down menus. Tick the Threshold is min/max option, set the threshold at 70, and change the red colour to dark blue using the Select Colour dialog box.

  15. With this yellow and blue colour scheme, the regions of high confidence are shaded blue and those of low confidence are shaded white and yellow.

 This exercise can be viewed in the Viewing AlphaFold Models in Jalview video.