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Transparency is used to adjust the transparency of Surfaces and Slices. (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. This allows different selections to have different transparencies on the same object (or also on different objects).

# load a random protein
fetch 1rty

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