May 8 2008
Contents
 
Introduction
Overview - RECOMMENDED READING FOR NEW ICM USERS
File Menu
Graphics Move Tools
Display Tab
Light Tab
Labels Tab
PDB Search Tab
Meshes Tab
View Menu
Selections
Tables
Sequences
Bioinfo Menu
Tools Menu - Xray
Tools Menu - 3D Predict
Tools Menu - Analysis
Tools Menu - Superimpose
Homology and Modelling
Working with Chemistry Tools
Chemsitry Menu
Docking
Animations, Slides, & Documents
 Animations
 Slides
  Navigation
  Add and Save
  Edit
  Move
  Effects
 Documents
Movie Making
Frequently Asked Questions
Tutorial - Graphical Display
Molecular Document
Tutorial - Working with PDB Protein Structures
Tutorial - Working with Sequence Alignments
Tutorial - Ligand Binding Pocket Analysis
Tutorial - Homology and Modeling Tools
Tutorial - Crystallographic Analysis Tools
Tutorial - Working with Chemical Tables
Tutorial - Working with the Molecular Editor
Tutorial - Chemical Searching
Tutorial - Docking and Virtual Ligand Screening
 
Index
PrevICM User's Guide
23.2 Making Molecular Slides
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[ Navigation | Add and Save | Edit | Move | Effects ]

The following information can be stored in a slide.

  • Viewpoint
  • Window layout
  • Current table(s)
  • Alignments
  • Annotations, labels, user-defined
  • HTML
  • Preferences for GRAPHICS.quality, ruler style, rocking state information
  • For each (mol.) object: representations and their colors, sites
  • For each grob (mesh): representation and colors.


To begin making ICM Molecular Slides:

  • First load the structure or structures you wish to display in your first slide. Additional structures, labels etc and text can be added at any point during the slide making process.
  • Slides can consist of Static views or Transitions and Animations.
  • Click on the camera button in the bottom panel of the ICM Graphical User Interface (see picture below).

  • Once you have clicked on the camera button you will see that the first slide has been generated. The first slide is shown in the ICM Workspace window as shown below.

  • A number of new buttons will also be displayed next to the camera button (see Slide Navigation)
  • You can generate as many slides as you require by clicking on the camera button.


To run a slide show

To optimally view a slide show select the buttons shown below:

NOTE: Slides are associated with the objects currently loaded into ICM. Therefore if you delete an object then the slides will not work. However if you delete an object and then re-read the same object with the same name and structure the slides will be ok.


To save a slide show

  • File/Save Project

23.2.1 Slide Navigation


You can make as many slides as you wish as described in the Making Molecular Slides section.

To navigate through the slides you can use the buttons shown below, the cursor keys for some operations or the right click options in the ICM Workspace.

The slide currently displayed is highlighted in red in the ICM Workspace.

To jump to another slide right click and select "Set Slide".

All slides are displayed in the ICM Workspace. You can hover the mouse over a slide name in the ICM Workspace and a thumbnail sketch of the slide is displayed as shown below. This can be used for slide navigation purposes.

Or you can right click on the name of the slide in the ICM Workspace and select the option "Preview".

23.2.2 Add and Save Slide


You can jump to the slide you wish to edit by following the slide navigation instructions.

To edit the content of a slide the procedure is to add a new slide and then delete the old one or use the "in place option " option:

  • Click and hold down on the camera button.

  • Select the option "Save Slide" and a data entry window as shown below will be displayed.

  • Enter the name of the slide
  • Enter a description of the slide.
  • If you wish to keep the current window layout check the box provided
  • Enter the location of the new slide in the series of slides either before,after or in place of
  • Enter the location (ie slide number) where you wish the edited slide to be placed.


To delete a slide:

  • Right click on the name of the slide in the ICM Workspace and select Delete.


To change the name of a slide

  • Right click on the name of the slide in the ICM Workspace and select Edit Slide.

23.2.3 Edit Slide Description


You can edit the description and visualization properties in the slide description dialog, which mimics the Save Slide dialog.

  • Click and hold on the "make slide button".
  • Select Edit Slide Description.

23.2.4 Move Slide


To change the slide's position in the slideshow use the Move Current Slide option and select the new position from the list.

  • Click and hold on the "make slide button".
  • Select Edit Slide Description.

  • Select the position in the slide show where you want to move the slide to.

23.2.5 Slide Effects


Smooth Transition from current slide to selected slide

  • Right click on the name of the slide in the ICM Workspace.
  • Select Edit Slide.
  • Select the desired transition effect - smooth or blend as shown below.
  • Select the length of the transition in milli seconds.

Co-display more than one slide

  • Right click on the name of the slide in the ICM Workspace you wish to co-display with the curently displayed slide.
  • Select the option co-display slide.


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