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  • DeepView – The Swiss-PdbViewer

    User Guide

    v. 3.7

    http://www.expasy.org/spdbv/

    DeepView – Swiss-PdbViewer user guide. Since there was a strong demand for a printable version of a DeepView user guide, we decided to prepare this manuscript to complements the documentation and tutorial found on the web site. We are aware that this user guide is still incomplete in some chapters, there are references missing, etc.

    Please help us to make this user guide useful for you: If you find any errors or inconsistencies, or you don't find an important piece of information, please let us know.

    The DeepView Team

    Geneva, 13 September, 2001

    GlaxoSmithKline R&D World Trade Center I Rte de l'Aéroport 10 1215 Geneva 15, Switzerland

    http://www.expasy.org/spdbv/

  • Contents

    Preface ...................................................................................................................................................iii

    Introduction............................................................................................................................................1 I. Overview ..........................................................................................................................................1 II. Working Environment.....................................................................................................................1

    Installing DeepView...............................................................................................................................4 I. Requirements and Installation ..........................................................................................................4 II. DeepView Directories .....................................................................................................................6

    STARTING a DeepView Session ..........................................................................................................9 I. Loading Files ....................................................................................................................................9 II. Displaying Windows .....................................................................................................................10 III. Obtaining Help.............................................................................................................................11

    Ending a DeepView Session ................................................................................................................13 I. Saving Data ....................................................................................................................................13 II. Closing DeepView ........................................................................................................................14

    Basic DeepView Commands................................................................................................................15 I. Using the Toolbar...........................................................................................................................16

    a. Using the tools............................................................................................................................17 b. Using the menus.........................................................................................................................21 c. Special commands......................................................................................................................28

    II. Using the Control Panel................................................................................................................29 Using the Layers Infos Window.........................................................................................................34

    Advanced DeepView Commands........................................................................................................37 I. Working on a Layer........................................................................................................................37

    a. Modifying commands ................................................................................................................38 b. Searching commands .................................................................................................................46 c. Computing commands ...............................................................................................................50 d. Crystallographic commands.......................................................................................................58

    II. Working on a Project ....................................................................................................................64 a. Merging commands....................................................................................................................67 b. Superposing commands .............................................................................................................68 c. Alignment commands ................................................................................................................73

    Homology Modeling.............................................................................................................................75 I. Loading Files ..................................................................................................................................77 II. Generating a Modeling-Project .....................................................................................................79 III. Submitting a Modeling-Project....................................................................................................83 IV. Evaluating and Improving the Model ..........................................................................................84

    Display Modes ......................................................................................................................................85 I. Non Stereoscopic Modes ................................................................................................................86 II. Stereoscopic Modes ......................................................................................................................88

    Setting Preferences ..............................................................................................................................91 I. Overview ........................................................................................................................................91 II. Setting Preferences........................................................................................................................92

    Annex 1: List of Key Modifiers and Menus.....................................................................................103

  • ii DeepViewManual

    I. Key Modifiers...............................................................................................................................103 II. List of Menus ..............................................................................................................................104

    Annex 2: Scripting Language ...........................................................................................................110 I. Using Scripts ................................................................................................................................110 II. Scripting Language .....................................................................................................................110 III. List of Commands......................................................................................................................113

    Annex 3: Hardware Requirements...................................................................................................130

    Annex 4: CALCULATIONS.............................................................................................................132 I. Connect.........................................................................................................................................132 II. Secondary structure detection .....................................................................................................132 III. Mutations ...................................................................................................................................132 IV. Building loops............................................................................................................................133 V. Molecular surfaces ......................................................................................................................133 VI. Electrostatic potentials...............................................................................................................133 VII. Electron density maps ..............................................................................................................134 VIII. Solvent accessibility................................................................................................................134 IX. Matrices .....................................................................................................................................135 X. Threading energy / mean force potential (PP) ............................................................................135 XI. FORCE FIELD ENERGY (FF).................................................................................................135 XII. transformation matrices ....................................................................