$ global name=transparency1
$ scene1 visualization=../TransAtlas.vmd 

# scene1

! transparencies work for VMD materials,
! so changing them has to be coordinated
! with the representation settings; also
! transparency/opacity can be partial,
! as set through start/limit

highlight         selection=sheet color=structure material=diffuse mode=u alias=bsheets
make_transparent  material=diffuse t=2s
make_opaque       material=diffuse t=2s
highlight         mode=d alias=bsheets
highlight         selection=helix color=structure material=diffuse mode=u alias=helix
make_transparent  material=diffuse t=2s limit=0.25
make_opaque       material=diffuse t=2s start=0.25
