[ Create | Edit | Insert Images | Insert Script | Dialog Box | Navigation | Protect ]

An ICM Molecular Document contains text and images which can be hyperlinked to the graphical display. Therefore by a single click of the mouse a representation described within the text can be instantly displayed. The hyperlinks are usually linked to a set of slides but can also be linked to a series of commands in a script.

25.3.1 Creating a Molecular Document

To begin creating an ICM document

• File/New/HTML
• Enter text (in standard HTML format if you wish) or plain text is fine. Formatting can be changed as described in the edit section below.
• Click OK

• A text panel will be displayed in the graphical user interface.

25.3.2 Editing a Molecular Document

To edit the HTML text in the graphical display

• First create an HTML document and the text panel will be displayed in the graphical user interface.
• Right click in the body of the text display panel.
• Select Edit Source
• At this point you can add text or change the formatting of the document.
• For example you may wish to make some text bold. To do this select the text you wish to make a bold.You can select text by clicking and dragging over the text - selected text will be highlighted in blue. Next right click and select Bold or press the 'B" button on the HTML Source Editor. The steps are shown below.

To make a hyperlink between the text and the graphical display (slide)

Easiest way to do this is to make a slide or set of slides of the graphical display you wish to link to. See Making Molecular Slides for help on this.Once slides have been created:

• File/New/Html
• Right click in the body of the text display panel.
• Select Edit Source
• Highlight the text you wish to link to a graphical display - you can do this by left clicking and dragging over the text (selected text will be highlighted in blue).
• Right click and select 'Insert Slide or Action' and a window as shown below will be displayed.

• Select the 'Display Slide:' option
• Select which number slide you wish the text to be linked to from the drop down menu.
• There is an option to display the slide as a thumbnail image in the text document panel. Check if appropriate.
• If you wish to have a smooth transition between this slide and the previous display - select the box - and then select the length of the transition in msecs.

OR (this is the old way of adding hyperlinks)

• Add the following anchor into the html code (e.g. using "Edit Source" option from the document's right-click menu):

<a> text here that will link to an ICM script  </a>

• Right click on the blue hyperlinked text
• Select "Add ICM Script"
• Enter a name for your script.
• Enter an ICM script related to the text.

To link text to a previously stored slide

• Right click on the blue hyperlinked text
• Select "Add ICM Script"
• Select Display Slide Button
• Select Slide number from drop down list

An example of the text display within an ICM document.

Any number of HTML doucments can be stored:

25.3.3 Insert Image

NOTE: The easiest way to add images (PNG or JPEG) into an ICM Document is to use drag and drop. You can drag and drop the image into the ICM Workspace or go to File/Open. Once the image is in the album in the ICM Workspace you can then drag it from the ICM workspace into tthe HTML editor.

Another way to insert a picture into the HTML text panel

• First read the image into the ICM photo album File/Open OR Drag and Drop from directory into the ICM Workspace.

The image name and preview will then be displayed in the ICM Workspace.

• Create HTML text - File/New/HTML. Add text.
• Right click in the HTML window and select 'Edit Source'.
• Right click on the position in the ICM Script Editor where you would like to insert the image.
• Select 'Insert Image'

• Select the image name source.
• Choose the desired Width and Height.
• Click OK.
• Click Save in the ICM Script Editor.

25.3.4 Insert Script

How to insert a script to the text panel

There are 3 ways to add a script - described in more detail below

1. Drag and drop script from ICM Workspace

2. In the HTML Source Editor - right click and select Insert Slide or Action

3. Create an "inline" script

These methods are described below:

Drag and Drop Method

• Create a script File/New/Script
• The script will be displayed in the ICM Workspace.
• Right click in the HTML Text Panel (for instructions on how to create this panel see create molecular document) and select edit source and the HTML Source Editor will be displayed.
• Click-Drag and Drop the script into the HTML Source Editor

A line as shown below will be added.

<a href="#icm/script/script1">text placed here will be displayed as a link in the document</a>

Another way to add a script to the document is to Insert Action:

• Right click in the body of the text display panel.
• Select Edit Source
• Highlight the text you wish to link to a graphical display - you can do this by left clicking and dragging over the text (selected text will be highlighted in blue).
• Right click and select 'Insert Slide or Action' or select the button in the HTML Source Editor and a window as shown below will be displayed.

• Select the option [Arguments and] ICM commands
• Add script in the editor provided
• Select ok

Inline Script

A script can be added to the HTML text in the following way

• Right click in the body of the text display panel.
• Select Edit Source
• Enter script in the format as shown below.

<!--icmscript name="script2"
#dialog{"Test"}
# i_number1 (2)
# i_number2 (3)
print $1 + $2
--><a name="script2" href="#_">script2</a>

25.3.5 Insert a Dialog Box

Dialog boxes are provided to enable a viewer to interact with a presentation or document file. The dialog box will be a gui data entry box. For an example here is a script to prompt the user of the file to enter a pdb code:

#dialog{"Read PDB File"}
# s_pdbcode (1crn)
read pdb $1 
ds a_1.

The code above can be saved as a script or inside the html text. To do this:

1. Right click on the HTML text display and select "Edit Source".
2. Highlight the text you wish to link to a dialog box and then select the right click and select 'Insert Slide or Action' or select the button in the HTML Source Editor and a window as shown below will be displayed.

OR.

1. Right click on the HTML text display and select "Edit Source".
2. Add a link to a script as shown below.

<a href="#icm/script/script1">Example Script 2</a> 

25.3.6 Document Navigation

The following buttons shown below aid document navigation. Also remember that more than one document can be stored and the header of each document file will be displayed in multiple tabs in the text panel window.

25.3.7 Protect Shell Objects From Deletion

When making a molecular document you can protect objects from deletion by the person who reads your document by:

• Right click on the object in the ICM Workspace.
• Select the Protect option.