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using the jmolScript function (this may be slighly out of date; I'm not up to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
<ee063...@live.com<mailto:ee063...@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
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