Prime User Manual - ISP

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120 West 45th Street, 29th Floor New York, NY 10036 Zeppelinstraße 13 81669 München, Germany 101 SW Main Street, Suite 1300 Portland, OR 97204 Dynamostraße 13 68165 Mannheim, Germany 8910 University Center Lane, Suite 270 San Diego, CA 92122 Quatro House, Frimley Road Camberley GU16 7ER, United Kingdom SCHRÖDINGER ®
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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
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Chapter 11: Command Syntax The alig
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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 and 152: sequences coloring.................
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