Prime User Manual - ISP

Contents
11.7 ssp—Secondary Structure Prediction............................................................. 107
11.8 sta—Single Template Alignment ...................................................................... 109
11.9 tfm—Tertiary Folding Module ........................................................................... 112
Chapter 12: Command-Line Utilities ..................................................................... 115
12.1 Multiple Template Alignment: structalign....................................................... 115
12.2 Format Conversion: seqconvert....................................................................... 116
12.3 Structure Preparation: primefix.py .................................................................. 118
12.4 Structure Alignment: align_binding_sites...................................................... 119
12.5 Database Update Utilities .................................................................................. 120
12.5.1 update_BLASTDB......................................................................................... 120
12.5.2 rsync_pdb ..................................................................................................... 120
Appendix A: Third-Party Programs ........................................................................ 121
A.1 Location of Third-Party Programs .................................................................... 121
A.1.1 BLAST/PSI-BLAST, Pfam, and the PDB......................................................... 121
A.1.2 Secondary Structure Prediction...................................................................... 121
A.2 Third-Party Program Use Agreement ............................................................... 122
Appendix B: Environment Variables ...................................................................... 123
Appendix C: File Formats ............................................................................................. 125
C.1 Input File Formats ............................................................................................... 125
C.2 Output File Formats ............................................................................................ 125
Appendix D: Error Messages and Warnings ................................................... 127
D.1 Input Sequence .................................................................................................... 127
D.2 Find Homologs ..................................................................................................... 127
D.2.1 Error Messages .............................................................................................. 127
D.2.2 Warnings in Homologs Table .......................................................................... 128
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