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Ellipsoid transparency
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Overview
This controls the level of Transparency with which PyMOL renders ellipsiods. Setting this to 0 means full opacity (no transparency); setting this to 1.0 means fully transparent.
Syntax
# set to a float in the range [0,1]
set ellipsoid_transparency, float
# for example, set it to 0.35
set ellipsoid_transparency, 0.35