Prime User Manual - ISP

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Chapter 4: Comparative Modeling: Edit Alignment
towards solvent. As you make changes to the alignment, click Update again to see how each
change has altered the mapping of the query’s residue properties onto the template structure.
If there are obvious errors in the alignment (such as gaps in regions of secondary structure), a
warning will appear in the Build Structure dialog box. Manual editing can be used to adjust the
alignment before attempting to build the structure again.
4.5.4 Updating the Step View Table
After the Align job is complete, the Step View table is updated with the new alignment score,
the percent identity, the percent similarity, and the percent gaps (all rounded to the nearest
integer). This information can be updated after any change, including manual editing of the
alignment, by clicking the Update button. The changed alignment is also reflected in the
Maestro Workspace display of the structure.
4.6 Error Messages
When you click Next at the end of the Edit Alignment step, the Check Alignment warning may
appear. The warning lists possible alignment problems that you may want to fix before
continuing to the next step. For example, gaps in secondary structure elements of the template,
or gaps in the query that are aligned to secondary structure elements of the template.
If you do not want to make corrections to the alignment, click Continue to go to the next step.
To make corrections based on the information in the error message, make a note of the gap
locations given, click Cancel to close the message box while remaining in Edit Alignment, and
change the alignment accordingly.
Prime 2.1 User Manual