Prime User Manual - ISP

4.3 Initial and Imported Alignments
Chapter 4: Comparative Modeling: Edit Alignment
4.3.1 Accepting the BLAST/PSI-BLAST Alignment
When you start the Edit Alignment step, the BLAST/PSI-BLAST alignment for the template
you selected in Find Homologs is displayed in the sequence viewer. See Figure 4.1.
If this is the template and the alignment you want to use, click Next and go to Build Structure.
To accept a different template, using its existing alignment, click on the desired template and
then click Next.
4.3.2 Exporting an Alignment
You may want to save the existing alignment for later use before making changes. Click the
Export button to the right of the Alignments table to open the Export Alignments To File panel.
To import the alignment again, see Section 4.3.3.
4.3.3 Importing an Alignment
Prime can also use an alignment generated in another program (or exported previously from
Prime). The sequences in the alignment file must be exactly the same as those used by Prime,
and so must the sequence and structure (PDB) names.
Note: The template PDB ID must be uppercase in the alignment file.
To import an alignment, click the Import button to the right of the Alignments table. This opens
the file selection window (Import Alignments From File). For details of the allowed formats, see
Appendix C.
4.4 Secondary Structure Predictions (SSPs)
4.4.1 Generating SSPs
A secondary structure prediction for the query is required to run the Align program. To run all
available SSP programs, click Run SSP. One secondary structure prediction program (SSpro)
is bundled with Prime. However, the optional third-party program PSIPRED is highly recommended
for optimal results, especially for GPCRs. PSIPRED is not available on Windows. See
Appendix A for more information on this program.
When the SSP run is finished, the secondary structure predictions are displayed in the sequence
viewer below the query sequence. If there is a problem running the structure prediction
programs, an error message is displayed.
Prime 2.1 User Manual 29