Prime User Manual - ISP

Chapter 3: Prime–Structure Prediction: Initial Steps
If the problem involves a template with multiple chains, you can use the getpdb utility (see
Section D.2.3 of the Maestro User Manual) to extract each chain into a separate .pdb file, then
run structure alignment again.
For information on running structure alignment from the command line, see Section 12.1.
3.2.6 Continuing to the Next Step
When you are satisfied with the template (or structurally aligned multiple templates) you have
selected, follow the Comparative Modeling Path by proceeding to the Edit Alignment step.
If no satisfactory templates can be identified by BLAST/PSI-BLAST and you have not
imported a template, you can follow the Threading Path by proceeding to the Fold Recognition
step.
Note: The maximum length of a query in the Threading Path is 1,000 residues. It is recommended
that such long sequences be divided into queries by probable domains, if this
has not been done already, and the homolog search be repeated for these shorter
queries before entering the Threading Path.
3.2.7 Saving Runs With Different Templates
If you decide later to try a different template, you can avoid overwriting your existing workflow
by starting a new one before you navigate back to Find Homologs to choose a different
homolog. Choose Save As from the File menu. This creates a copy of the current run, allowing
you to select a new template and build on it. You can then compare results from each run.
3.2.8 Error Messages
If there is an error, a message appears when you click Next to go to the next step. See
Section D.2 on page 127 for a list of error messages for Find Homologs.
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