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Command: transparency

transparency  spec   percent  [ what | target  string ]

The transparency command sets the transparency of atomic representations, molecular surfaces, and volume (map) isosurfaces to the specified percent, where 0% is completely opaque and 100% is completely transparent, without otherwise changing colors. There are limitations in rendering transparency. See also: color, surface, volume, material, per-model clipping

The target option allows acting on only a subset of the possible displays of a given atom, residue, etc. The string can be any combination of the following letters, without commas or spaces:

The default is target s, surfaces only.

Alternatively, the targets (what to act upon) can be specified with one or more of the following keywords as a comma-separated list at the end of the command:


Make chain A molecular surface 50% transparent:
transparency /A 50
Make atoms 75% transparent:
transparency 75 target a
– or –
transparency 75 atoms
Turn off transparency of atoms and cartoons for the current selection:
transparency sel 0 target ac
Make model #2 chain B ribbons 80% transparent:
transparency #2/B 80 target r
– or –
transparency #2/B 80 ribbon

UCSF Resource for Biocomputing, Visualization, and Informatics / April 2024