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Prime User Manual - ISP

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Chapter 4: Comparative Modeling: Edit Alignment<br />

contains bad data or the sequence doesn’t match the query sequence, an error message is<br />

displayed.<br />

4.4.3 Deleting or Editing an SSP<br />

If you believe an SSP is incorrect, you may delete it entirely or edit the incorrect portions. To<br />

delete an SSP, right-click on the SSP and choose Delete from the shortcut menu.<br />

To edit an SSP:<br />

1. Click the Edit SSP toolbar button:<br />

2. Highlight the part of the SSP you want to change.<br />

3. Type the character e, h, or -.<br />

E represents strand, H represents helix, and – represents loop.<br />

The highlighted region of the prediction is changed to your choice.<br />

4.4.4 Resetting SSPs<br />

To retrieve an unmodified SSP after editing, click Run SSP. This immediately resets the SSP,<br />

but does not rerun the prediction programs.<br />

4.5 Generated and Modified Alignments<br />

4.5.1 Running the Align Program<br />

Before running an alignment, if you want to take advantage of the special capabilities for<br />

aligning GPCRs, select Align GPCRs. These capabilities include fingerprint matching, a<br />

customized GPCR sequence database, and identification of transmembrane helices.<br />

To take advantage of expert knowledge, one or more pairs of query/template residues that you<br />

know should be aligned can be constrained to remain so, by using alignment constraints.<br />

To constrain a pair of residues to remain aligned:<br />

1. Click the Add Anchors toolbar button.<br />

<strong>Prime</strong> 2.1 <strong>User</strong> <strong>Manual</strong> 31

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