Prime User Manual - ISP

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Chapter 6: Fold Recognition
To delete an SSP, right-click on the SSP in the sequence viewer and choose Delete from the
shortcut menu.
To edit an SSP:
1. Click the Edit SSP toolbar button:
2. Highlight the part of the SSP you want to change.
3. Type the character e, h, or -.
E represents strand, H represents helix, and – represents loop.
The highlighted region of the prediction is changed to your choice.
6.2.4 Resetting SSPs
To retrieve an unmodified SSP after editing, click Run SSP. This immediately resets the SSP
(but does not rerun the prediction programs).
6.3 Searching for Templates
When you are satisfied with the SSP profile for the query, click Search to run the Fold Recognition
program. You may prefer to change the search options described in the following section
before doing so.
6.3.1 Search Program Options
Display of Results
Show Top N Results
By default, the 100 top-ranked templates found are shown in the Templates table. This number
can be changed in the Show Top N Results text box before clicking Search.
Z-Scoring
Searching can be done with or without Z-scoring. The Z-score shows how significant a match
is relative to a random match. It is calculated by shuffling the query sequence. See Section 9.2
on page 71 for more information on Z-score filtering.
Prime 2.1 User Manual