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Hermes User Guide - Cambridge Crystallographic Data · PDF fileHermes User Guide ix About This User Guide

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  • Hermes User GuideA Component of the GOLD Suite

    5.6.1 GOLDSuite Release

    Copyright 2018 Cambridge Crystallographic Data Centre

    Registered Charity No 800579

  • ii Hermes User Guide

    Conditions of Use

    The GOLD suite of programs (the "Program") comprising all or some of the following: Hermes (including as Relibase+ client and as SuperStar interface), GOLD, associated documentation and software, are copyright works of CCDC Software Limited and its licensors and all rights are protected. Use of the Program is permitted solely in accordance with a valid Software Licence Agreement or a valid Licence and Support Agreement with CCDC Software Limited or a valid Licence of Access to the CSD System with CCDC and the Program is proprietary. All persons accessing the Program should make themselves aware of the conditions contained in the Software Licence Agreement or Licence and Support Agreement or Licence of Access Agreement.

    In particular: The Program is to be treated as confidential and may NOT be disclosed or re-

    distributed in any form, in whole or in part, to any third party. No representations, warranties, or liabilities are expressed or implied in the supply

    of the Program by CCDC Software Ltd., its servants or agents, except where such exclusion or limitation is prohibited, void or unenforceable under governing law.

    GOLD 2017 CCDC Software Ltd.

    Hermes 2017 CCDC Software Ltd.

    Implementation of ChemScore, Heme, Kinase and Astex Statistical Potential scoring functions and the Diverse Solutions code within GOLD 2001-2013 Astex Therapeutics Ltd.

    All rights reserved

    Licences may be obtained from:

    CCDC Software Ltd.12 Union RoadCambridge CB2 1EZUnited Kingdom

    Web: www.ccdc.cam.ac.ukTelephone: +44-1223-336408Email: [email protected]

  • Hermes User Guide iii

    Contents

    About This User Guide ...................................................................................................................ix

    1 Overview of the Hermes Visualiser ...................................................................................1

    2 Introduction to Using the Hermes Visualiser.....................................................................2

    2.1 Overview of the Interface.....................................................................................2

    2.2 Top-Level Menu....................................................................................................2

    2.3 Picking Modes.......................................................................................................4

    2.4 Right-Clicking ........................................................................................................4

    2.5 Resetting the Display ............................................................................................4

    2.6 Several Ways of Doing Things...............................................................................5

    3 Loading Structures, and Hits from Other Programs ..........................................................6

    3.1 Loading Structures and Files from Other Programs .............................................6

    3.2 Loading a Structure from a File ............................................................................6

    3.3 Deleting Structures...............................................................................................6

    4 Navigating Proteins with the Molecule Explorer Window .................................................8

    4.1 The Main Purpose of the Molecule Explorer Window ..........................................8

    4.2 Opening the Molecule Explorer Window..............................................................8

    4.3 Using the Molecule Explorer Window ..................................................................8

    4.3.1 Overview of the Molecule Explorer Display Layout ..............................8

    4.3.2 Using the Molecule Explorer to Control What is Displayed ..................9

    4.3.3 Using the Molecule Explorer to Make Atom Selections......................10

    4.3.4 Using the Molecule Explorer to Change Display Properties................14

    4.3.5 Using the Molecule Explorer to Centre and Zoom with respect to an entry....................................................................................................15

    4.3.6 Using the Molecule Explorer to control Label display.........................15

    5 Moving the Contents of the 3D Display Area ..................................................................16

    5.1 Translating the Contents of the 3D Display Area................................................16

    5.2 Rotating the Contents of the 3D Display Area....................................................16

    5.3 Flipping the Display by 90 Degrees.....................................................................16

    5.4 Scaling the Display ..............................................................................................16

    5.5 Changing the Display Perspective.......................................................................17

    5.6 Moving Structures Independently of One Another ............................................17

    5.7 Setting the Rotation Centre................................................................................17

    6 Selecting and Deselecting Atoms and Molecules ............................................................18

    6.1 The Purpose of Selecting Atoms and Molecules ................................................18

    6.2 Ways of Selecting Atoms and Molecules............................................................18

    6.3 Making Complex Selections: Defining Subsets of Protein Atoms.......................19

    6.3.1 The Purpose of Protein Subsets ..........................................................19

  • iv Hermes User Guide

    6.3.2 Creating Protein Subsets.....................................................................19

    6.3.3 Visualising Saved Protein Subsets .......................................................21

    6.4 Identifying Selected Atoms.................................................................................21

    7 Customising the Display ..................................................................................................23

    7.1 Setting General Display Properties.....................................................................23

    7.1.1 Setting Lighting Effects........................................................................23

    7.1.2 Setting Background Colours................................................................23

    7.1.3 Depth Cueing ......................................................................................23

    7.1.4 Z-Clipping ............................................................................................24

    7.2 Setting Default Style and Colour Preferences for Different Parts of the Protein24

    7.3 Altering Structure Display Properties Globally ...................................................25

    7.3.1 Altering the Display Style Globally ......................................................25

    7.3.2 Altering the Colouring Scheme Globally .............................................25

    7.3.3 Switching Hydrogens On and Off Globally ..........................................25

    7.3.4 Switching Unknown Atoms On and Off Globally.................................25

    7.3.5 Displaying or Undisplaying Bond Types Globally ................................26

    7.4 Setting Display Properties for Particular Atom(s) or Bond(s) .............................26

    7.5 Using Display-Property Dialogue Boxes..............................................................26

    7.5.1 Using the Show/hide Dialogue Box.....................................................26

    7.5.2 Using the Select Color Dialogue Box ...................................................27

    7.6 Element and Bond-Type Display Conventions....................................................28

    7.6.1 Standard Element Colours ..................................................................28

    7.6.2 Bond-Type Display Conventions .........................................................29

    8 Labelling Atoms ...............................................................................................................30

    8.1 Types of Labels ...................................................................................................30

    8.2 Turning All Atom Labels On or Off......................................................................30

    8.3 Labelling Individual Atoms and Sets of Atoms....................................................30

    8.4 Customising the Appearance of Labels...............................................................32

    8.4.1 Setting the Colours of Labels ..............................................................32

    8.4.2 Setting Label Sizes...............................................................................32

    8.4.3 Setting Label Fonts..............................................................................32

    8.4.4 Moving and Optimising Label Positions ..............................................32

    9 Calculating and Displaying Ribbons, Tubes and Other Graphics Objects ........................33

    9.1 Creating Centroids ..............................................................................................33

    9.2 Setting the Display Properties of Centroids........................................................33

    9.3 Deleting Centroids .............................................

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