Prime User Manual - ISP

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28 Chapter 4: Comparative Modeling: Edit Alignment Prime 2.1 User Manual Figure 4.1. The Edit Alignment panel, initial view. If you want to search for a family that best matches the query sequence, but did not do so in the Find Homologs step, click Find Family to run HMMER/Pfam. For more information on this option, see Section 3.2.2 on page 20. When you are satisfied with the alignment, click the Next button to proceed to the Build Structure step.
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
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Prime User Manual Appendix A: Third
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Prime User Manual Appendix D: Error
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!UNUSABLE: SEQRES numbering is wron
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Prime User Manual Getting Help Schr
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Getting Help If Maestro fails, an e
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Prime User Manual Glossary Chapter
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K killing jobs ....................
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sequences coloring.................
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