Dear Juliana --

does anyone know how to set transparency to a small portions of a molecule: for example, in a 150-aa molecule, set the first 10 residues to be transparent?

I don't know if what you are asking is possible, but here is how I'd do:

create short_part, i. 1:10
set transparency, 0.6
set transparency, 0.5, short_part

you then have 2 different transparency settings for your molecule, and for the residues 1 to 10, respectively.

HTH
Kind regards.

Leo
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Chavas Leonard, Ph.D.
Research Associate
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Faculty of Life Sciences
The University of Manchester
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