Rabia,
"Highlight" is a very vague word…there are a few different things you can do. Generically speaking, you need to "select" the atoms you want to do something with, then style them. This is a very common workflow in Jmol.

For starters, try playing around with the "show structure" command. Right-click in the applet and select "Console," then type "show structure." That command gives you a list of secondary structural elements, which you can select individually using "select strucno = #" (replace "#" with a number). You can select by atom using select atomno, or by residue using select resno.

To style, a wide variety of commands are available. To start simple, after selecting try "color green." 

All Jmol scripting commands can be executed programmatically in Javascript using the jmolScript function (this may be slighly out of date; I'm not up to speed on JS object developments in Jmol).

Cheers, Mike

On Sep 5, 2012, at 2:01 AM, MUHAMMAD HASEEB <ee063099@live.com>
 wrote:

IM A RESEARCHER AT QUAID-E-AZAM UNIVERSITY
AND AM CREATING A TOOL FOR ANNOTATION AND SUPERPOSITION OF MOTIFS,
I WANT TO HIGHLIGHT A SPECIFIC MOTIF IN THE STRUCTURE OF IT PROTEIN,
IM USING THE JMOL APPLET
NEED HELP 
UNABLE TO PERFORM THE HIGHLIGHTING
PLEASE HELP

REGARDS 
RABIA HASEEB
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats.http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers