Prime User Manual - ISP

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Contents
Prime 2.1 User Manual
3.2.5 Multiple Templates and Structure Alignment..................................................... 23
3.2.6 Continuing to the Next Step .............................................................................. 25
3.2.7 Saving Runs With Different Templates.............................................................. 25
3.2.8 Error Messages................................................................................................. 25
Chapter 4: Comparative Modeling: Edit Alignment....................................... 27
4.1 The Comparative Modeling Path .......................................................................... 27
4.2 Overview of the Edit Alignment Step................................................................... 27
4.3 Initial and Imported Alignments ........................................................................... 29
4.3.1 Accepting the BLAST/PSI-BLAST Alignment ................................................... 29
4.3.2 Exporting an Alignment..................................................................................... 29
4.3.3 Importing an Alignment..................................................................................... 29
4.4 Secondary Structure Predictions (SSPs)............................................................ 29
4.4.1 Generating SSPs .............................................................................................. 29
4.4.2 Exporting and Importing SSPs.......................................................................... 30
4.4.3 Deleting or Editing an SSP ............................................................................... 31
4.4.4 Resetting SSPs................................................................................................. 31
4.5 Generated and Modified Alignments ................................................................... 31
4.5.1 Running the Align Program............................................................................... 31
4.5.2 Align Program Technical Details ....................................................................... 33
4.5.3 Manually Editing the Alignment......................................................................... 33
4.5.4 Updating the Step View Table ........................................................................... 34
4.6 Error Messages........................................................................................................ 34
Chapter 5: Comparative Modeling: Build Structure ...................................... 35
5.1 The Build Process ................................................................................................... 35
5.2 Preparing to Build ................................................................................................... 36
5.2.1 Multiple Templates (Set Template Regions)...................................................... 36
5.2.2 Including Ligands and Cofactors....................................................................... 37
5.2.3 Build Options..................................................................................................... 37
5.2.4 Omitting Structural Discontinuities .................................................................... 37