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:
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.
transparency 80,a,r ligand zr>5- make the atoms/bonds and ribbon segments of residues that are more than 5 Å from ligand 80% transparent
transp 75,s #3:60-100 frames 50- make the molecular surface patches of residues 60-100 in model 3 75% transparent over 50 frames