Jmol Help Page

This is a part of an assignment for Molecular Biology or Immunology at Davidson College.

There are a couple things you need to know before inserting a PDB file into a web page.

1) Jmol is a Java applet which means it is a small program that has to be downloaded to your computer before you can view any structures. Once you have viewed one structure, you will not have to download Jmol again until next time you log on.

2) Java programs require certain files to be in their proper location. Therefore, you need to know where to point to these files. For biology courses at Davidson, you must include this text in your web page at the code level, not the design level:

<applet name='Test_Protein' code='JmolApplet' archive='JmolApplet.jar' codebase='../../../../Immunology/jmol'
width='95%' height='80%' mayscript='true' >
<param name='progressbar' value='true' />
<param name='progresscolor' value='blue' />
<param name='boxmessage' value='Loading...' />
<param name='emulate' value='chime' />
<param name='bgcolor' value='#000000' />
<param name='load' value='
1SVC.pdb' />
<param name='script' value=";
select all ;

zoom 110;
wireframe 70;
move 0 -360 0 0 0 0 0 0 3 60;

" />

The red text must be in your page. The purple text is the name of your file. In the case of my test page, the pdb file is called "1SVC.pdb". Do not change any of the text, except the name of your file. The blue text is optional, and used to change the view. Zoom, wireframe and move (automatic rotation) are not required, but may allow you to present a particular view.

3) You must upload your pdb file and put it in your main folder along with your html files. This is also true of any figure files.


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