An Introduction To The ICM Graphical User Interface.

Slides:



Advertisements
Similar presentations
Step-by-Step: Add a Graphical Hyperlink USE the Special Events Final presentation that is still open from the previous exercise. 1.Go to slide 4, and click.
Advertisements

Presented by: Benefits Systems Support. Getting Started ê Open Powerpoint, create a blank presentation. ê Select a style for your first slide from the.
EXCEL Spreadsheet Basics
Microsoft Word 2010 Lesson 1: Introduction to Word.
475 Wall Street, Princeton NJ Introduction to PSCAD © 2012 Nayak Corporation Inc. 1.
CREATING A MULTIPLE PAGE REPORT Presented by: Dr. Ennis-Cole.
Word Processing First Steps
PowerPoint Practice Exercise
COE201 – Computer Proficiency Mr. Hamze Msheik
Chapter 10—Creating Presentations
Advanced Microsoft Word Hosted by Jared Hoffman Topics Keyboard Shortcuts Customizing Toolbars and Menus Auto Format & Auto Correct Tabs Inserting Pictures.
Microsoft Excel 2010 Chapter 7
XP New Perspectives on Microsoft Office Access 2003, Second Edition- Tutorial 2 1 Microsoft Office Access 2003 Tutorial 2 – Creating And Maintaining A.
Create slices and hotspots Create links in Web pages Create rollovers from slices Create basic animation Add tweening symbol instances to create animation.
Copyright 2007, Paradigm Publishing Inc. POWERPOINT 2007 CHAPTER 1 BACKNEXTEND 1-1 LINKS TO OBJECTIVES Create Presentation Open, Save, Run, Print, Close,Delete.
Creating And Maintaining A Database. 2 Learn the guidelines for designing databases When designing a database, first try to think of all the fields of.
Creating, Formatting, and Editing a Word Document with a Picture
1 Introduction to the Visual Studio.NET IDE Powerpoint slides modified from Deitel & Deitel.
Key Applications Module Lesson 12 — Word Essentials
ExitTOC Run & Route Directions 2003 Editing Run and Route Directions Edulog.nt v9.2 Use the buttons to navigate the training package First PagePreviousNextLast.
PowerPoint Lesson 2 Notes Working With Slides. Creating a New Presentation From a Theme 1.When preparing for a presentation, the best place to start is.
With Alex Conger – President of Webmajik.com FrontPage 2002 Level I (Intro & Training) FrontPage 2002 Level I (Intro & Training)
Review of last session The Weebly Dashboard The Weebly Dashboard Controls your account and your sites Controls your account and your sites From here you.
Power Point EDU 271 Microsoft PowerPoint is a powerful tool to create professional looking presentations and slide shows. PowerPoint allows you to construct.
Getting Started with Expression Web 3
Introduction to PowerPoint 2003 Learning And Research Technical Unit (LARTU)
Microsoft Word 2010 Chapter 1 Creating, Formatting, and Editing a Word Document with Pictures.
© Ms. Masihi.  The Dreamweaver Welcome Screen first opens when you start Dreamweaver.  This screen gives you quick access to previously opened files,
Key Applications Module Lesson 19 — PowerPoint Essentials
Creating a Presentation
PowerPoint. Basic Vocabulary Slide - Presentation - Slide layout – ► ► ► ► a single page in PowerPoint all the slides for a speech all the slides for.
Learning Microsoft Power Point Getting Started  There are three features that you should remember as you work within PowerPoint 2007: the Microsoft.
Microsoft PowerPoint Getting Started Guide Prepared for Towson University Dr. Jeff M. Kenton Amy Chase Martin 2007.
XP New Perspectives on Microsoft Office FrontPage 2003 Tutorial 4 1 Microsoft Office FrontPage 2003 Tutorial 4 – Using Shared Borders and Themes.
Creating a PowerPoint Presentation
Website Development with Dreamweaver
XP New Perspectives on Microsoft Access 2002 Tutorial 21 Microsoft Access Tutorial 2 – Creating And Maintaining A Database.
Create Forms Lesson 5. Objectives Software Orientation The Forms group (below) is located on the Create tab in the Ribbon and can be used to create a.
Dreamweaver CS4 Concepts and Techniques Chapter 2 Adding Web Pages, Links, and Images.
CREATING A POWERPOINT PRESENTATION. Planning a presentation Create a presentation Rearrange and delete text and slides Add animations Add transitions.
Review of last session Add text to your website Add text to your website Title Title Paragraph Paragraph Title and paragraph Title and paragraph Add photographs.
Basic Editing Lesson 2.
USING WORDPRESS TO CREATE A WEBSITE (RATHER THAN A BLOG) STEP-BY-STEP INSTRUCTIONS.
Introduction to Microsoft publisher
Joyelle White January 28, 2008 University of Phoenix EDTC 560 Dr. Eli MS Word 2007 Training.
Chapter 2 – Introduction to the Visual Studio .NET IDE
Moving and Copying Text Instructor: Glenda H. Easter ITSW 1401, Intro to Word Processing.
Basic Editing Lesson 2.
Fall 2003Sylnovie Merchant, Ph.D. ACCESS Tutorial Note: The purpose of this tutorial is to provide an introduction to some of the functions of ACCESS in.
By: Ms. Abeer Helwa 1. CREATE A WORD DOCUMENT 2 Blank document Templates To create a new blank document: click the File tab and click Blank document.
PowerPoint Practice Exercise 1.Save this file on your computer. 2.Open this file in PowerPoint 3.Edit each slide according to the instructions provided.
Chapter 4. Learning outcomes This Chapter will partially cover the learning outcome No. 2 i.e. Design presentations that use animation effects. (L02)
Dreamweaver MX. 2 Tools for Code Editing (p. 366) n An HTML editor like Dreamweaver writes most of the code you need, but at times you will need to perform.
Microsoft PowerPoint Prepared by the Academic Faculty Members of IT.
PowerPoint Basics Tutorial 2: A Slide Show In this tutorial you’re going to create a presentation from scratch. You will have to keep this presentation.
Word and the Writing Process. To create a document 1.On the Start menu, point to Programs, and then click Microsoft Word. A new document opens in Normal.
Chapter 11 Collaboration Features for Workbooks Microsoft Excel 2013.
 2002 Prentice Hall. All rights reserved. 1 Introduction to the Visual Studio.NET IDE Outline Introduction Visual Studio.NET Integrated Development Environment.
MS WORD INFORMATION TECHNOLOGY MANAGEMENT SERVICE Training & Research Division.
Chapter 10 Using Macros, Controls and Visual Basic for Applications (VBA) with Excel Microsoft Excel 2013.
Chapter 7 Creating Templates, Importing Data, and Working with SmartArt, Images, and Screen Shots Microsoft Excel 2013.
Key Applications Module Lesson 12 — Word Essentials Computer Literacy BASICS.
Chapter 11 Enhancing an Online Form and Using Macros Microsoft Word 2013.
Key Applications Module Lesson 12 — Word Essentials
Technology ICT Core: PowerPoint.
Introduction to PowerPoint
Microsoft Office Access 2003
Key Applications Module Lesson 12 — Word Essentials
Presentation transcript:

An Introduction To The ICM Graphical User Interface

Upper toolbars/ menus Lower toolbar/ menus Side toolbar Workspace panel Command line terminal HTML documents 3D graphics window MAIN ICM COMPONENTS

 The 3D window has several ‘hot-zones’ (marked as red boxes in the figure), which provides access to operations that change the scene’s view; Move the cursor into one of these zones to change the dragging function of your mouse.  All the functions described below assumes clicking + holding on the button indicated (i.e. dragging): move = rotation up/down = zoom in/out up/down = clip back plane up/down = clip front plane up/down = clip back+front planes Left button move = selection (markers appear); select empty zones to remove selection Right button move = translation Middle button Works while the cursor is on ‘rotation’ mode 3D Graphics Window Shortcuts

A. Loading molecules (2 ways): A. Loading molecules (2 ways): 1. drag&drop the PDB file into workspace or 2. File  Load  PDB  PDB Type in the PDB code Check this option Uncheck these two options & press OK B. Converting to ICM format: B. Converting to ICM format: 1. right-click on an object and pick ‘Convert PDB’ 2. On the following dialogue, uncheck all the boxes and press ‘OK’ Load a PDB File

Clicking here turns everything under it on, using the default settings (i.e. amino-acid chains as ribbons, ligands as xsticks, ions as CPK, etc.) Clicking here turns only this chain (molecule level) on. Displaying a Structure

2. Click here. Ribbons representation of the chain (chain a) will appear. Many green crosses representing the components of the selection will appear as well. Each shows you an atom within the selection. 3. Click here to clear the selection (and get rid of the green crosses) 1. Double-click the text; background of the line will turn grey Displaying Structures

1. Left-click + hold will open a menu providing other options (shown here) Left-click to add a slide immediately after the presently active (slide ‘2’ will be added in this example). Last slide (click to display) Current slide (pull menu to choose) First slide (click to display) Slide navigation buttons (previous/ next) Slide layout button 2. Pick ‘save slide’ for extra options when saving slides Saving Slides

Type in the name of the slide. Normally a few descriptive words such as ‘active site’, ‘mutation’, ‘alternate loop conformation’, etc. Check this box if you are preparing the ‘default’ slide or any other slide where the windows distribution is different from the slide-mode. Check both transition effects boxes for an iSee slide and change the values to the ones shown in the picture (2000 ms for smooth; 1000 ms for blend). \ Finish with the OK button. The position in the stack (order) where the new slide should be inserted can be defined here. Saving Slides

Selection levels (4 levels)Selection modes (4 modes) Representation modes (6 modes) Selections and Representations

You can expand protein/ peptide chains to see the residues by clicking on the ‘+’ sign by the chain. Then left-click + drag to select residues. You can add non- contiguous residues by holding ‘CTRL’ key while selecting. If there are elements being displayed, you can also select in the graphic window directly. Either change to the selection tools or with your mouse in ‘rotation’ mode, right-click + hold + drag to add to your selection. Selections and Representations

Find your ligand and right-click to launch the menu – then pick ‘ligand pocket’. This will automatically generate the pocket (surface) surrounding the selected molecule. To display labels, side chains and hydrogen bonds, check the box on the following dialogue box. Pocket is displayed as a 3D mesh - (representation mode can be changed by right-click on the mesh display box) If made from a converted PDB, pocket will be coloured (green: aliphatic, blue: HB donor; red: HB acceptor) Active Site Ligand Pocket

Find your ligand and right-click to launch the menu – then pick ‘extract ligand(s)’. You’ll be offered option to extract as 2D or 3D. Pick 2D and a table will be generated with the ligand(s). On the new table, right-click on the compound and on the menu pick ‘save/export image’. You can then copy the image to an internal album or save it as a image to be used in other programs (e.g. Powerpoint). Extract Ligand

Make a selection (see previous sections) and click on either the residue or atom label buttons. If the position of the label needs to be changed, click and hold on the label button and check ‘drag labels’. This activates the dragging hotspot on every label: Adding Labels

Pre-defined colours: Right-click = to set the background colour Left-click = to set the representation colour ! Warning: left-clicking when there is no selection = everything displayed will be coloured. Pre-defined colours: Right-click = to set the background colour Left-click = to set the representation colour ! Warning: left-clicking when there is no selection = everything displayed will be coloured. Colour wheel: preset colouring schemes – applied to the selection (if no selection, will be applied to everything displayed in the screen) Some useful schemes: - NtoC: from N- to C-terminus of a protein, starting as blue and changing to red. - Bfactor: maps the B-factors (when available) to the structure (low=blue; high=red) - Chain: automatically assigns a different colour for each chain Colour wheel: preset colouring schemes – applied to the selection (if no selection, will be applied to everything displayed in the screen) Some useful schemes: - NtoC: from N- to C-terminus of a protein, starting as blue and changing to red. - Bfactor: maps the B-factors (when available) to the structure (low=blue; high=red) - Chain: automatically assigns a different colour for each chain Coloring

For any of the representation button, left-click and hold to be presented with additional options – colour amongst them. The colour tool is exactly the same as the one shown above. Note that the colour will apply to the selection AND the chosen representation only. If nothing is selected, then everything being displayed using the chosen representation will be coloured. For any of the representation button, left-click and hold to be presented with additional options – colour amongst them. The colour tool is exactly the same as the one shown above. Note that the colour will apply to the selection AND the chosen representation only. If nothing is selected, then everything being displayed using the chosen representation will be coloured. Coloring According To Properties

2. Right-click on any of the green selection crosses and pick the ‘annotate selection’ option. 3. Type in the site tag name (and optionally a longer description – not recommended: tends to clutter the screen). 5. Tag hot spot 2: Middle-click + drag: moves the head of arrow (in 3D space) 5. Tag hot spot 2: Middle-click + drag: moves the head of arrow (in 3D space) 4. Tag hot spot 1: Left-click: cycles through site description modes. Middle-click + drag: moves the end of arrow (in 3D space). 4. Tag hot spot 1: Left-click: cycles through site description modes. Middle-click + drag: moves the end of arrow (in 3D space). 1. Make a selection of residue(s) Single residue: right-click over residue. Multiple res.: right-click + hold + drag to select, then right-click on the selection to activate menu. 1. Make a selection of residue(s) Single residue: right-click over residue. Multiple res.: right-click + hold + drag to select, then right-click on the selection to activate menu. Adding Sites

1. Start by preparing the representation. Anything 3D on the screen will be captured (ribbons, sticks, CPK, skins, other meshes, etc.). Text will not be captured. The orientation doesn’t matter: the grob to be generated will be a 3D object, so it can be reposition it later. ! Make sure that all elements to be captured in the grob are visible on-screen. 1. Start by preparing the representation. Anything 3D on the screen will be captured (ribbons, sticks, CPK, skins, other meshes, etc.). Text will not be captured. The orientation doesn’t matter: the grob to be generated will be a 3D object, so it can be reposition it later. ! Make sure that all elements to be captured in the grob are visible on-screen. 2. Enter the following command in the terminal: make grob image 2. Enter the following command in the terminal: make grob image Meshes – Graphical Objects (Grob)

In the command line window, a message will be displayed giving the name of the new grob. Change it as soon as it is created to allow you to track them. Right-click on the name of the newly-created grob, pick ‘rename’ from the menu and then type the new name In the command line window, a message will be displayed giving the name of the new grob. Change it as soon as it is created to allow you to track them. Right-click on the name of the newly-created grob, pick ‘rename’ from the menu and then type the new name Check the result: undisplay everything and right- click on the square in front of your new grob. Representation styles available: dot, wire (wireframe), smooth surfaces, rugged surfaces and transparent smooth surfaces. Wire and transparent surfaces are useful if you want to show what’s underneath. Check the result: undisplay everything and right- click on the square in front of your new grob. Representation styles available: dot, wire (wireframe), smooth surfaces, rugged surfaces and transparent smooth surfaces. Wire and transparent surfaces are useful if you want to show what’s underneath. Meshes – Graphical Objects (Grob)

Without occlusionWith occlusion Occlusion shading adds shadow according to accessibility: the less accessible, the darker the shadow. Right-click on the mesh and pick ‘occlusion shading’ from the options. A new dialog appears - change the value to determine the level of shading. Occlusion shading adds shadow according to accessibility: the less accessible, the darker the shadow. Right-click on the mesh and pick ‘occlusion shading’ from the options. A new dialog appears - change the value to determine the level of shading. Meshes – Graphical Objects (Grob)

1. In the workspace, identify the ligand to be shown with elec. density and double-click on it to select it: 2. tools  Xray  Contour Electron Density 1. In the workspace, identify the ligand to be shown with elec. density and double-click on it to select it: 2. tools  Xray  Contour Electron Density 3. In the new dialogue box, pull down to select the EDS map. 4. Correct the sigma level for density contouring to In the new dialogue box, pull down to select the EDS map. 4. Correct the sigma level for density contouring to 1.0. Start loading an electron density map – a.Tools  Xray  Get Electron density map... or b.Drag & drop a CCP4 format density map into the workspace Electron Density

5. A new mesh with the density has been created, but all the density around the ligand is also displayed – you might want to clear that up a bit and display only density for the ligand. 6. To do so, right-click on the density mesh  split 5. A new mesh with the density has been created, but all the density around the ligand is also displayed – you might want to clear that up a bit and display only density for the ligand. 6. To do so, right-click on the density mesh  split ICM will now take the mesh and look for continuity. Everything that is continuous will be separated as a new mesh. 7. The results are sorted according to size. Normally your ligand’s density is the largest, so enter a low number in the split dialogue box. ICM will now take the mesh and look for continuity. Everything that is continuous will be separated as a new mesh. 7. The results are sorted according to size. Normally your ligand’s density is the largest, so enter a low number in the split dialogue box. Electron Density

8. now that the main mesh has been split, click on each one of the new meshes to find the one that wraps around your ligand. Your scene is much cleaner now. Electron Density

1. Display both molecules in the screen. 2. Select both molecules (you’ll see green crosses). 3. Click on the ‘superimpose’ button. Superimpose

1. Superimpose works only on the object/ molecule level. It doesn’t affect meshes. However when a superimpose is performed, ICM stores the transfrmation matrix into the variable ‘R_out’. 1. Superimpose works only on the object/ molecule level. It doesn’t affect meshes. However when a superimpose is performed, ICM stores the transfrmation matrix into the variable ‘R_out’. 2. In the terminal, enter the following command: transform R_out Note: the command needs to be executed immediately after the superimpose operation (otherwise the R_out variable might be updated with output from other operations). 2. In the terminal, enter the following command: transform R_out Note: the command needs to be executed immediately after the superimpose operation (otherwise the R_out variable might be updated with output from other operations). Transpose

1. Right-click in the HTML document and select the ‘edit’ option. There are two ways of starting a HTML document: 1. Drag&drop an external HTML file in the workspace 2. Open a new one with File  New  Pick the ‘HTML’ tab 3. Type in a title for your annotation/ HTML document; check the ‘pop in Brwoser’ option and finalise with ‘OK’. 4. Right-click in the HTML document and select the ‘edit’ option. If you have started a new one from scratch, then the content will be blank. Adding Text in the HTML Editor

2. The usual text editor tools will appear. At the same time, the main window is ready to accept typed or pasted text / elements. 3. If the panel is too narrow, some of the tools will be hidden. These can be accessed by resizing the HTML panel or by clicking on this button 4. When you re done, remember to save the modifications. Note: this save operation saves the HTML within the ICM project, but is not saving the entire project (with all the loaded elements, etc.). Adding Text in the HTML Editor

1. Right-click anywhere on a HTML document  edit to start the HTML editor 2. Locate the text to have an ICM link added to it and select it (left-click hold + drag). 3a. On the selected text, Right-click  Insert  Insert Slide and a new dialog will open. 3b. Alternatively click the little camera icon on the HTML editor icons bar. 2. Locate the text to have an ICM link added to it and select it (left-click hold + drag). 3a. On the selected text, Right-click  Insert  Insert Slide and a new dialog will open. 3b. Alternatively click the little camera icon on the HTML editor icons bar. Linking Text To Slides

2. Use the pull down menu to pick the desired slide. 3. Select and delete the word ‘smooth’. 4. Finish with ‘OK’. Your text has been now linked to the selected slide. 1. Pick the ‘Slide’ tab. 3. Pick now the ‘ICM script’ tab. Linking Text To Slides

Simply click on the save button to save. Usual saving options (e.g. Save as, etc.) will be made available in the dialogue box that opens. Everything loaded into ICM and created during your session (a ‘project’) can be bundled into a single ICM binary file (extension.icb ). The.icb file can now be used by any version of ICM, running in any of the supported Operating Systems and also as a web-browser plug-in. For downloads of the programs and plug-ins, please visit: Saving a Project