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QUANTA 2006 X-Ray Structure and Analysis MAY 2006

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QUANTA 2006 X-Ray Structure and Analysis MAY 2006 QUANTA 2006 X-Ray Structure and Analysis MAY 2006 Copyright (1) Copyright Copyright ©2006, Accelrys Software Inc. All rights reserved. The Accelrys® name and logo are registered trademarks of Accelrys Software Inc. This product (software and/or documentation) is furnished under a License/Purchase Agreement and may be used only in accordance with the terms of such agreement. (2) Trademark The registered trademarks or trademarks of Accelrys Software Inc. include but are not limited to: ACCELRYS® & ACCELRYS Logo, ACCORD, BIOSYM®, CATALYST®, CERIUS®, CERIUS2®, CHARMM®, CHEMEXPLORER®, DIAMOND DISCOVERY®, DISCOVER®, DISCOVERY STUDIO®, DIVA®, FLEXSERVICES®, GCG®, GENEATLAS®, INSIGHT®, INSIGHT II®, MACVECTOR®, MATERIALS STUDIO®, OMIGA®, QUANTA®, SEQARRAY, SEQFOLD®, SEQLAB®, SEQMERGE®, SEQSTORE®, SEQWEB®, TOPKAT®, TSAR®, UNICHEM®, WEBKIT, WEBLAB®, WISCONSIN PACKAGE®. All other trademarks are the property of their respective holders. (3) Restrictions on Government Use This is a “commercial” product. Use, release, duplication, or disclosure by the United States Government agencies is subject to restrictions set forth in DFARS 252.227-7013 or FAR 52.227-19, as applicable, and any successor rules and regulations. (4) Acknowledgments, and References To print photographs or files of computational results (figures and/or data) obtained using Accelrys software, acknowledge the source in an appropriate format. For example: “Computational results obtained using software programs from Accelrys Software Inc. Dynamics calcula- tions performed with the Discover program using the CFF forcefield, ab initio calculations performed with the DMol3 program, and graphical displays generated with the Cerius2 molecular modeling system.” To reference an Accelrys publication in another publication, Accelrys Software, Inc., is the author and the pub- lisher. For example: Accelrys Software Inc., Cerius2 Modeling Environment, Release 4.8, San Diego: Accelrys Software Inc., 2006. (5) Request for Permission to Reprint and Acknowledgment Accelrys may grant permission to republish or reprint its copyrighted materials. Requests should be submitted to Accelrys Scientific Support, either through electronic mail to [email protected], or in writing to: Accelrys Scientific Support 10188 Telesis Court, Suite 100 San Diego, CA 92121 Please include an acknowledgement “Reprinted with permission from Accelrys Software Inc., Document name, Month Year, Accelrys Software Inc., San Diego.” For example: Reprinted with permission from Accelrys Software Inc., Cerius2 User Guide, June 2006, Accelrys Software Inc.: San Diego. Contents Preface: How to Use This Book . 1 How to find information . 2 Typographical conventions . 2 1. Introduction to X-Ray Structure Analysis and Refinement 5 Accelrys’ X-Ray crystallography applications . 6 X-POWERFIT . 6 X-AUTOFIT . 6 X-BUILD. 6 3D notebook and other tools . 6 CNX . 7 X-SOLVATE . 7 X-LIGAND. 7 The crystallographic structure determination process . 8 Before you begin . 8 Collect and process data. 9 Determine phases. 9 Generate initial model . 10 Build and refine model. 10 Refinement . 10 Adding ligands. 10 Add solvent and refine final model. 10 Assess model . 11 2. Using the X-applications . 13 Introduction . 13 Application subdivision . 13 Electron density Bones . 14 Mask generation. 15 Cα tracing . 15 Adding Cα trace atoms. 15 Moving Cα trace atoms. 16 Moving Cα-trace segments . 16 Cα trace polarity . 17 Sequence assignment . 17 Loading sequences . 17 Sequence assignment . 18 Unique sequence . 18 Cα-trace -> all atom model . 19 Chain polarity . 19 Where do the coordinates go?. 19 Model building . 20 Refinement . 20 Grid refinement. 21 Gradient refinement . 21 Monte Carlo refinement . 22 Geometry refinement . 22 Model building protein/NA . 22 Model build ligands and waters . 23 QUANTA 2006 X-Ray Structure and Analysis i General comments . 23 Validation . 23 3. Managing Maps . 25 Interactive Map generation . 25 Typical Use . 26 Maps Management table . 27 Menu bar . 28 Maps menu. 28 Import . 28 Add a Map. 29 Delete a Map . 29 Replace a Map . 29 List Maps . 29 Hide Table. 29 Contour menu . 30 Contour Maps . 30 Contour Mode. 30 Characteristics of Display Lines . 30 Define Contour Levels . 31 Utils menu . 32 Purge Contours . 32 Reset Drawing . 32 Edit line . 32 Column headings . 33 Rows . 33 Managing maps in various QUANTA applications. 34 X-LIGAND, X-SOLVATE: . 34 X-POWERFIT, X-AUTOFIT: X-BUILD: . 35 4. Introduction to X-AUTOFIT/X-BUILD/X-POWERFIT (X-FIT) 37 Map generation . 37 Map contouring . 37 Density skeletonization . 38 Solvent masks . 38 3D text editor . 38 Automated Cα tracing . 38 Cα tracing . 39 Automated sequence assignment and fuzzy logic assignment 39 Cα trace --> all-atom model . 39 Model building . 39 Refinement techniques . 40 Validation techniques . 40 Data logging . 41 Data integrity . 41 X-AUTOFIT in QUANTA. 41 Memory requirements for X-AUTOFIT . 41 Accessing X-AUTOFIT . 43 General X-AUTOFIT and X-BUILD behavior . 44 Using multiple structures and maps in X-AUTOFIT . 44 Palettes and tool activity in X-AUTOFIT . 45 Dial box . 47 Graph windows . 47 Tables . 48 ii QUANTA 2006 X-Ray Structure and Analysis 5. Using X-AUTOFIT . 49 Solvent boundaries or map masks . 49 Parameterization . 50 Editing bones . 50 Generating a mask . 51 Editing masks . 51 Summary . 51 Bones . 52 Displaying and skeletonizing an electron density map.52 Determining map quality . 53 To get information about map quality . 53 Improving map quality . 53 Modifying the skeletonization initial cut-off parameter54 To adjust the Start parameter . 54 Adjusting branch trimming parameters . 55 To adjust branch parameters . 55 Using bones with masks . 55 Deleting bones points . 56 To delete bones points . 56 To change the strand type . 56 Bones and symmetry . 56 Using bones with Cα-tracing . 57 Cα-tracing . 57 Generating Cα segments using assisted carbon building58 To generate a new segment . 58 Editing segment and Cα atoms . 59 Using the pseudo-Ramachandran plot. 60 Positioning the next Cα atom . 62 Evaluating and changing segment polarity . 63 To evaluate segment polarity . 63 To change segment polarity . 63 Cut/paste Cα segments . 64 To join two segments . 64 Cutting segments . 64 Templates and rigid body editing of Cα traces . 64 Sequence assignment . 65 Reading in sequence information. 65 Fitting a sequence to a segment . 65 Generating sequence alignment information . 66 Redefining the weights . 68 Creating new definitions . 69 Finding unique sequences . 69 Predicting secondary structure . 70 Building all-atom representation from Cα.
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