Hello Phil, and welcome to Jmol!

Let's see:

> <script type="text/javascript">
> jmolCheckbox("script ./Pgradsorted", "script ./reset", "Chain P" )
> </script>

This is OK, but the "script" command assumes that the following is the name of 
a file. From 
your description, I am not sure if you have a plain-text file with the name 
"Pgradsorted" and 
another named "reset" (both with no extension). Please make sure of that first. 
Maybe 
having a file extension like "spt" or "txt" helps (it shouldn't make a 
difference, but particularly 
from a web server extensions sometimes matter).


> my script Pgradsorted contains2 commands per amino acid ~ 200 commands

OK, as long as you mean "your script file", as I said above.


> the top 10 lines of the script are:-
> $ head Pgradsorted

I don't see what this $ line is, but it may be blocking Jmol from reading the 
content as a 
script, since it will not understand that "command".
Apart from that, everything looks good.

In case that's what you wanted, the way to tell Jmol "this is a comment, ignore 
it" is either a 
# sign or a double forward slash, //

Try to open the Java console and see any errors there.

Good luck, and don't hesitate to come back with more details


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