Prime User Manual - ISP

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Prime User Manual Copyright © 2009 Schrödinger, LLC. All rights reserved. While care has been taken in the preparation of this publication, Schrödinger assumes no responsibility for errors or omissions, or for damages resulting from the use of the information contained herein. Canvas, CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike, and WaterMap are trademarks of Schrödinger, LLC. Schrödinger and MacroModel are registered trademarks of Schrödinger, LLC. MCPRO is a trademark of William L. Jorgensen. Desmond is a trademark of D. E. Shaw Research. Desmond is used with the permission of D. E. Shaw Research. All rights reserved. This publication may contain the trademarks of other companies. Schrödinger software includes software and libraries provided by third parties. For details of the copyrights, and terms and conditions associated with such included third party software, see the Legal Notices for Third-Party Software in your product installation at $SCHRODINGER/docs/html/third_party_legal.html (Linux OS) or %SCHRODINGER%\docs\html\third_party_legal.html (Windows OS). This publication may refer to other third party software not included in or with Schrödinger software ("such other third party software"), and provide links to third party Web sites ("linked sites"). References to such other third party software or linked sites do not constitute an endorsement by Schrödinger, LLC. Use of such other third party software and linked sites may be subject to third party license agreements and fees. Schrödinger, LLC and its affiliates have no responsibility or liability, directly or indirectly, for such other third party software and linked sites, or for damage resulting from the use thereof. Any warranties that we make regarding Schrödinger products and services do not apply to such other third party software or linked sites, or to the interaction between, or interoperability of, Schrödinger products and services and such other third party software. June 2009
Contents Document Conventions ..................................................................................................... ix Chapter 1: Introduction ....................................................................................................... 1 1.1 The Prime Suite in Maestro ..................................................................................... 1 1.2 Prime Documentation............................................................................................... 2 1.3 Running Schrödinger Software .............................................................................. 3 1.4 Citing Prime in Publications.................................................................................... 3 Chapter 2: Using Prime–Structure Prediction .................................................... 5 2.1 Prime Runs and Maestro Projects.......................................................................... 5 2.2 General Panel Layout................................................................................................ 7 2.3 The Prime Menu Bar ................................................................................................. 9 2.3.1 The File Menu ..................................................................................................... 9 2.3.2 The Edit Menu................................................................................................... 10 2.3.3 The Display Menu ............................................................................................. 10 2.3.4 The Step Menu ................................................................................................. 12 2.4 The Prime Toolbar ................................................................................................... 13 2.5 Prime Job Options and Control ............................................................................ 14 2.5.1 The Job Options Dialog Box ............................................................................. 14 2.5.2 Setting Up and Launching Jobs ........................................................................ 14 2.5.3 Monitoring Jobs................................................................................................. 15 2.5.4 Adding Structures to the Project Table.............................................................. 16 Chapter 3: Prime–Structure Prediction: Initial Steps ................................... 17 3.1 Input Sequence Step............................................................................................... 18 3.2 Find Homologs Step ............................................................................................... 19 3.2.1 Importing Homologs.......................................................................................... 19 3.2.2 Searching for Homologs.................................................................................... 20 3.2.3 Find Homologs Search Options ........................................................................ 21 3.2.4 Search Results.................................................................................................. 22 Prime 2.1 User Manual iii
Page 1: Prime User Manual Prime 2.1 User Ma
Page 5 and 6: Contents 5.3 Running the Build Stru
Page 7 and 8: Contents 11.7 ssp—Secondary Struc
Page 9 and 10: Document Conventions In addition to
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
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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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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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