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Transparency is used to adjust the transparency of Surfaces. (For other transparencies in PyMOL, see Cartoon Transparency, Sphere Transparency, and Stick Transparency.


set transparency, F, selection

where F is a floating point number in the range [0.0 - 1.0], where selection is the selected surface to apply the change to (for examples, see below).

For the value of F, 1.0 will be an invisible and 0.0 a completely solid surface.


Whole Surface

Change the transparency of the whole surface to 50%.

# show all surfaces with 50% transparency.
set transparency, 0.5

Selected Surface Elements

Simple example showing how to do partial surface transparency

# load a random protein
fetch 1rty

# set the partial transparency for the selected residues
set transparency, 0.65, i. 1-100