Hello Moon

There are a couple of web applications that do that, but it is not an easy task.
Please, let us know in more detail what you need. For example, do you know in 
advance 
what is the sequence you want highlighted, or is this a generic need that 
should work with 
any protein?

For example, you can select a known sequence using the "select 
within(sequence)" 
command
See 
http://chemapps.stolaf.edu/jmol/docs/#atomexpressionsfunctions
or 
http://chemapps.stolaf.edu/jmol/docs/#atomexpressions  >  Functions  > WITHIN

and then apply whatever highlight you want: halos, spacefill, a color...
Will that be enough for your needs?





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