Examples of how to use color altloc in general are at:

http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/altloc.htm

I tested it with loading two separate models in two separate frames, and 
that worked, too..

Perhaps if you can send me a url to a page that does not work, I can 
take a closer look at your
particular implementation.

Bob Hanson

saravanan wrote:

> Hi,
> I want to do superimposition of two protein structures in Jmol.
> Is it possible, I loaded the molecules and executed the command, 
> "frame all",
> now i can see the two protein but with different orientations, i want 
> to do superimposition and when i coloured them by "colour altloc", its 
> colouring all molecules in "green" colour..
>  
> P.Saravanan
>
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