At this stage, it makes good strategy to continue manually Confirming links, automatically Extending them, and manually Confirming them to overcome hurdles the automation cannot handle.
For the data shown in these figures, the thing to do now is extend in the C-terminal direction. In the Fragments panel, clicking on cluster 77 brings you to that cluster, and you find there’s a probable link to cluster 31, but its score, 1.60, is below the 2.20 threshold used by the Extend algorithm. If you click Confirm to link clusters 77 and 31, then click Extend, you should see another handy stretch of residues becomes automatically linked and assigned:
When you are sure you wish to keep the assignments for this stretch, click the “Freeze” button just below the “Extend” button. Don’t worry. If you want to reconsider your commitment to these assignments, you can click the ‘Thaw” button, and they will become more flexible again. Freezing assignments send the assignment data to the Assign…Atoms table, which can be written to a text file. Freezing also disable your ability to link to frozen clusters.
Clicking “Freeze” turns the letters in your Sequence display back to black and draws lines over and under the frozen, assigned region:
You can see the results of freezing in the Atom Assignments panel by clicking from the main toolbar: “Assign…Atoms.”
Figure 33. Calling up the Atom Assignments panel
Selecting “Assign…Atoms” will give you the panel showing chemical shift assignments for all the atoms in the protein, subject to you filtering specifications. In the figure below, the filter is set so all CA and CB atoms are displayed.
