Usage:
transparency  percent[,a][,f][,r][,s][,v][,l][,la][,lr][,lb][,b]  atom-spec  [ frames N ]

Usage:
~transparency[,a][,f][,r][,s][,v][,l][,la][,lr][,lb][,b]  atom-spec  [ frames N ]

The transparency command sets transparency to the specified percent, where 0% is completely opaque and 100% is completely transparent. It can affect atoms, bonds, ring fill, ribbons, labels (3D), and various surfaces. The frames option indicates making the change gradually over N frames. The ~transparency command sets transparency to 0%. See the video mini-example. See also: colordef, color, modelcolor, scolor, rainbow, rangecolor, background, movie-related commands

The assignment can be restricted with one or more specifiers:

• a - atoms (and normally, bond halves match the flanking atoms; see b for bonds-only control)
• f - ring fill
• r - ribbons
• s - molecular surfaces and nonmolecular surface models; equivalent to using surftransparency
• v - VDW surfaces
• l - atom and residue labels
• la (or al) - atom labels
• lr (or rl) - residue labels
• lb (or bl) - bond labels
• b - bonds only (not the flanking atoms); however, bond-only transparency will not be visible unless halfbond mode has been turned off, for example, by using color with the ,b specifier

The atom-spec indicates which atoms (and/or associated bonds, ribbon segments, surface patches, etc.) should be affected, and a similar specification can be used for nonmolecular surface models. If no specification is given, all applicable items are affected.

Except for molecular surfaces, subsequent color changes will reset transparency to zero.

Examples:

transparency 80,a,r ligand zr>5

transp 75,s #3:60-100 frames 50