Prime User Manual - ISP

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The script provides a recommendation for each template, and provides some information on
the alignment.
6.5 Building a Model
Based on the recommendations of the script, you can use the Comparative Modeling path to
build a model on any of the suitable templates. To do so, the template must be exported and
read back into Prime, which you can do with the following procedure:
1. In the Fold Recognition step, include the template in the Workspace (click the V column).
2. Click the Create entry from Workspace main toolbar button to create a project entry.
3. Export the project entry as a PDB file.
4. In the Structure Prediction panel, create a new run and read in the query sequence again.
5. Click Next.
6. In the Find Homolog step, import the saved template PDB file.
There is no need to run Search because a template was manually imported.
7. Select the imported template, and follow the Comparative Modeling path (or click Edit
Alignment in the Guide).
8. In the Edit Alignment step, click Import SSP and select the .casp SSP files that you used
for the analysis.
9. Click Align to run the alignment.
From this point, you can continue to the Build Structure step as normal.
Prime 2.1 User Manual