Jul 3 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
Local DB
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
Ligand Editor
Animations, Slides, & Documents
ActiveICM
Movie Making
Frequently Asked Questions
Tutorial - Graphical Display
Molecular Document
 Making a Molecular Document
 Tut moldoc transition
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
30.1 Making a Molecular Document
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In this example we will show the key steps to make a molecular document which links text to the graphical display.

Step 1: Adding text to HTML window.

  • File/New and select the Html tab.
  • Enter the name you wish to call your html document
  • Click OK

  • You will see a new html panel displayed as shown below.

  • Right click in the Html panel and select "Edit Source". An HTML Source Editor as shown below will be displayed.

  • To change the text formatting click and drag over the text so it is highlighted in blue and then use the buttons in the editor or the option in the right click menu.

NOTE:Images can be added to the document please see the section of the manual entitled "insert image" in the Animations, Slides and Documents chapter.

Step 2: Add a selection of slides you wish to link text to or display in your molecular document.

For instuctions on how to make slides please see the section of the manual entitled "making molecular slides".

Step 3: How to link text to slides

  • Right click in the Html panel and select "Edit Source". The HTML Source Editor as shown above will be displayed.
  • Select the text you wish to link to a slide and right click.
  • Select "Insert Slide or Action and a data entry box as shown below will be displayed.
  • Enter an internal link name.
  • Check the Display Slide button.
  • Select which slide you would like to link to.
  • Do you want to see the slide as a thumbnail in the text panel? If so check the appropriate box.
  • Do you want to see a smooth transition to this slide? If so select how long you want the transition to last for in msecs. ICM will automatically interpolate between the slides.
  • Click OK and your hyperlinked text will be displayed in blue in the text panel.

Step 4: How to link text to an action such as a series of ICM commands.

  • Right click in the Html panel and select "Edit Source". The HTML Source Editor as shown above will be displayed.
  • Select the text you wish to link to a an ICM command.
  • Select "Insert Slide or Action and a data entry box as shown below will be displayed.
  • Enter an internal link name.
  • Select the [Arguments and] ICM commands option
  • Enter your Arguments or ICM script.


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