Prime User Manual - ISP

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viii Contents D.3 Edit Alignment ...................................................................................................... 129 D.4 Build Structure ..................................................................................................... 129 D.5 Refinement ............................................................................................................ 129 Getting Help ........................................................................................................................... 131 Glossary.................................................................................................................................... 135 Index ............................................................................................................................................ 137 Prime 2.1 User Manual
Document Conventions In addition to the use of italics for names of documents, the font conventions that are used in this document are summarized in the table below. Font Example Use Sans serif Project Table Names of GUI features, such as panels, menus, menu items, buttons, and labels Monospace $SCHRODINGER/maestro File names, directory names, commands, environment variables, and screen output Italic filename Text that the user must replace with a value Sans serif uppercase CTRL+H Keyboard keys Links to other locations in the current document or to other PDF documents are colored like this: Document Conventions. In descriptions of command syntax, the following UNIX conventions are used: braces { } enclose a choice of required items, square brackets [ ] enclose optional items, and the bar symbol | separates items in a list from which one item must be chosen. Lines of command syntax that wrap should be interpreted as a single command. File name, path, and environment variable syntax is generally given with the UNIX conventions. To obtain the Windows conventions, replace the forward slash / with the backslash \ in path or directory names, and replace the $ at the beginning of an environment variable with a % at each end. For example, $SCHRODINGER/maestro becomes %SCHRODINGER%\maestro. In this document, to type text means to type the required text in the specified location, and to enter text means to type the required text, then press the ENTER key. References to literature sources are given in square brackets, like this: [10]. Prime 2.5 User Manual ix
Page 1 and 2: Prime User Manual Prime 2.1 User Ma
Page 3 and 4: Contents Document Conventions .....
Page 5 and 6: Contents 5.3 Running the Build Stru
Page 7: Contents 11.7 ssp—Secondary Struc
Page 11 and 12: Prime User Manual Chapter 1: Introd
Page 13 and 14: 1.3 Running Schrödinger Software C
Page 15 and 16: Prime User Manual Chapter 2: Using
Page 17 and 18: Chapter 2: Using Prime-Structure Pr
Page 23 and 24: Guide Chapter 2: Using Prime-Struct
Page 27 and 28: Prime User Manual Chapter 3: Prime-
Page 29 and 30: 3.2 Find Homologs Step Chapter 3: P
Page 31 and 32: To identify a family for the query
Page 33 and 34: Table 3.1. Homologs table data Colu
Page 35 and 36: Chapter 3: Prime-Structure Predicti
Page 37 and 38: Prime User Manual Chapter 4 Chapter
Page 39 and 40: 4.3 Initial and Imported Alignments
Page 41 and 42: Chapter 4: Comparative Modeling: Ed
Page 43 and 44: 4.5.2 Align Program Technical Detai
Page 45 and 46: Prime User Manual Chapter 5 Chapter
Page 47 and 48: Chapter 5: Comparative Modeling: Bu
Page 53 and 54: Prime User Manual Chapter 6: Fold R
Page 55 and 56: Figure 6.2. The Fold Recognition pa
Page 57 and 58: 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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Chapter 11: Command Syntax • Outp
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Table 11.5. Keywords for the multir
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Chapter 11: Command Syntax It is no
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Table 11.6. General keywords for th
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Table 11.7. Protocol-specific keywo
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SKA has difficulty aligning to mult
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Table 11.8. Keywords syntax for ska
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Chapter 11: Command Syntax ........
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Chapter 11: Command Syntax The foll
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Chapter 11: Command Syntax aligned
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Files Chapter 11: Command Syntax In
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Prime User Manual Chapter 12: Comma
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Table 12.1. Keywords for the seqcon
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Chapter 12: Command-Line Utilities
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Prime User Manual Appendix A: Third
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Prime User Manual Appendix B: Envir
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Prime User Manual Appendix C: File
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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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Symbols + (plus sign), in Pfam sequ
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K killing jobs ....................
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sequences coloring.................
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120 West 45th Street, 29th Floor Ne
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