DNA Double Helix Structure

Title

Introductory Note

First Topic

<> first subtopic
- <> list items
<> second subtopic
- <> list items
<> third subtopic
- <> list items

Second Topic

<> Load new Pdb and script UL>

three HTML files,

at least 1 pdb file

and associated script files

for maintaining sanity - place these files together in a unique directory.

The HTML object used to load the plug-in is called "EMBED", and it has various parts. A typical embed object might look something like this:

<embed src="filename" height=hpixels width=wpixels [lots of options]>
- one very useful option is name="your_text", which identifies the plug-in for manipulating it from other HTML files
- another is script="command 1; command 2; etc;" which sends script commands to the plug-in for the initial display of the coordinate file src="filename"

Example - (note that there are no real scripts for this file, and clicking on the script buttons will trigger your browser to ask if you want to get a plug-in - ignore that!)

The first file I have called Main.htm.

This is the file that one loads in order to see the Chime / Netscape page, and is thus the one that you might link to in a table of contents or other HTML document that points to your page.

It sets up the frameset that will split the Browser window into two parts

the one one the left is for the plug-in Chime
the one on the right is for text and buttons that send script files to the plug-in in the left frame

Here is example HTML code for Main.htm

<HTML><HEAD><TITLE>Main Frameset</TITLE></HEAD>
<FRAMESET COLS="355,*" BORDER=1> <FRAME SCROLLING="auto" NAME="ImagePane" RESIZE="YES" BORDER=1 MARGINWIDTH=2 MARGINHEIGHT=2 SRC="Image.htm"> <FRAME SCROLLING="auto" NAME="TextPane" RESIZE="YES" BORDER=1 MARGINWIDTH=2 MARGINHEIGHT=2 SRC="Text.htm"> </FRAMESET>
<BODY></BODY> </HTML>

The second file I've called Image.htm.

This file

is loaded into the first frame, and
loads within itself an instance of the plug-in Chime
- the plug-in runs in a centered window that is
  - 350 pixels wide
  - 350 pixels tall
  - and bounded by two horizontal rules
naming the plug-in instance "FILE" so that script files can be sent to it from the next file 'Text.htm'
and sending it an initial pdb file and script commands

Here is the example HTML code for Image.htm

<HTML><HEAD><TITLE>TITLE</TITLE></HEAD> <BODY><CENTER><H3>Title</H3></CENTER> 

<HR ALIGN="CENTER" SIZE="3" WIDTH="80%">
<EMBED name="file" align=abscenter width=350 height=350 spiny=20 startspin=false display3D=sticks color3D=structure BGCOLOR="#000000" script="reset;slab off;select all;wireframe off;color structure;cartoons on;" SRC="/597a/stdnts98/pub/frames/file.pdb">
<HR ALIGN="CENTER" SIZE="3" WIDTH="80%">
The images displayed in this frame require the <A HREF="http://www.mdli.com/chemscape/chime/download.html" TARGET="_parent">Chemscape Chime</A> plug-in.  

 Coordinates from file.pdb.

</BODY></HTML>

Finally, the third file I've called Text.htm.

This file

presents the narative that guides the reader
- this narative can have images etc as in any HTML document
provides buttons to launch scripts that are sent to the plug-in called "FILE" as defined in the HTML code that was loaded into frame 1
note that the "embed" tag is preceded by << and ended by >>

The following example Text.htm file, with several buttons for launching hypothetical script files, looks awkward. Basically, you are using ordinary HTML coding as always, but embedding push buttons that will send script files to the plug-in when pushed. I have tried to illustrate an outline of the "style" for this template using bold and red lettering. Check out the real file to see what it looks like in a browser (but remember, it was intended to be viewed from main.htm)

<HTML><HEAD><TITLE></TITLE></HEAD> <BODY> <BIG><BIG><BIG> Title </BIG></BIG></BIG> Introductory Note 
<BIG><BIG>First Topic</BIG></BIG> <UL> <LI><<EMBED src="file1.spt" width=15 height=15 align=absmiddle button="push" target="FILE">> <BIG>first subtopic</BIG> <UL> <LI><<EMBED src="file2.spt" width=15 height=15 align=absmiddle button="push" target="FILE">> list items </UL> <LI><<EMBED src="file3.spt" width=15 height=15 align=absmiddle button="push" target="FILE">> <BIG>second subtopic</BIG> <UL> <LI><<EMBED src="file4" width=15 height=15 align=absmiddle button="push" target="FILE">> list items </UL> <LI><<EMBED src="file5.spt" width=15 height=15 align=absmiddle button="push" target="FILE">> <BIG>third subtopic</BIG> <UL> <LI><<EMBED src="file6.spt" width=15 height=15 align=absmiddle button="push" target="FILE">> list items </UL> </UL> <BIG><BIG>Second Topic</BIG></BIG> <ul> <li><<EMBED src="file7.spt" width=15 height=15 align=absmiddle button="push" target="file">> first subtopic.etc

.etc

</BODY>
</HTML> R> RG 1 123 32.552 21.082 15.685 1.00 49.69