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Official Release PyMOL v2.4 has been released on May 20, 2020.
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New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
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Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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== Overview ==

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 ..→

A Random PyMOL-generated Cover. See Covers.