Prime User Manual - ISP

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142 Index View Structure............................................. 12, 14 W warnings...................................... 18, 23, 127–129 workflow ....................................................... 9, 17 Prime 2.5 User Manual Workspace........................................... 10, 14, 136 Z Z-Score...................................................... 46, 136
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Prime User Manual Prime 2.1 User Ma
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Contents Document Conventions .....
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Contents 5.3 Running the Build Stru
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Contents 11.7 ssp—Secondary Struc
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Document Conventions In addition to
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Prime User Manual Chapter 1: Introd
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1.3 Running Schrödinger Software C
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Prime User Manual Chapter 2: Using
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Chapter 2: Using Prime-Structure Pr
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Guide Chapter 2: Using Prime-Struct
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Prime User Manual Chapter 3: Prime-
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3.2 Find Homologs Step Chapter 3: P
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To identify a family for the query
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Table 3.1. Homologs table data Colu
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Chapter 3: Prime-Structure Predicti
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Prime User Manual Chapter 4 Chapter
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4.3 Initial and Imported Alignments
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Chapter 4: Comparative Modeling: Ed
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4.5.2 Align Program Technical Detai
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Prime User Manual Chapter 5 Chapter
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Chapter 5: Comparative Modeling: Bu
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Prime User Manual Chapter 6: Fold R
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Figure 6.2. The Fold Recognition pa
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Figure 6.3. The Fold Recognition-Op
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Chapter 6: Fold Recognition potenti
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Prime User Manual Chapter 7: Prime-
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Chapter 7: Prime-Refinement If your
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7.2 Using the Refinement Panel Chap
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2. Click New Membrane (Auto-Place).
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Figure 7.3. The Refine loops task i
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Chapter 7: Prime-Refinement Figure
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Figure 7.6. The Structure Refinemen
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Chapter 7: Prime-Refinement The tex
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Chapter 7: Prime-Refinement ment, w
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7.11 Output of Refinement Jobs Chap
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Prime User Manual Chapter 8: Maestr
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Alignment Section Chapter 8: Maestr
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Chapter 8: Maestro Protein Structur
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Prime User Manual Chapter 9: Dockin
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Chapter 9: Docking Covalently Bound
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Prime User Manual Chapter 10: Prime
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Table 10.1. Options for the prime_m
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Prime User Manual Chapter 11: Comma
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Table 11.2. Keywords for the blast
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Table 11.3. Keywords for the bldstr
Page 101 and 102: Chapter 11: Command Syntax The alig
Page 103 and 104: Chapter 11: Command Syntax • Outp
Page 105 and 106: Table 11.5. Keywords for the multir
Page 107 and 108: Chapter 11: Command Syntax It is no
Page 109 and 110: Table 11.6. General keywords for th
Page 111 and 112: Table 11.7. Protocol-specific keywo
Page 113 and 114: SKA has difficulty aligning to mult
Page 115 and 116: Table 11.8. Keywords syntax for ska
Page 117 and 118: Chapter 11: Command Syntax ........
Page 119 and 120: Chapter 11: Command Syntax The foll
Page 121 and 122: Chapter 11: Command Syntax aligned
Page 123 and 124: Files Chapter 11: Command Syntax In
Page 125 and 126: Prime User Manual Chapter 12: Comma
Page 127 and 128: Table 12.1. Keywords for the seqcon
Page 129 and 130: Chapter 12: Command-Line Utilities
Page 131 and 132: Prime User Manual Appendix A: Third
Page 133 and 134: Prime User Manual Appendix B: Envir
Page 135 and 136: Prime User Manual Appendix C: File
Page 137 and 138: Prime User Manual Appendix D: Error
Page 139 and 140: !UNUSABLE: SEQRES numbering is wron
Page 141 and 142: Prime User Manual Getting Help Schr
Page 143 and 144: Getting Help If Maestro fails, an e
Page 145 and 146: Prime User Manual Glossary Chapter
Page 147 and 148: Symbols + (plus sign), in Pfam sequ
Page 149 and 150: K killing jobs ....................
Page 151: sequences coloring.................
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