Crystallography‎ > ‎Molecular graphics‎ > ‎Pymol‎ > ‎


Transparent sticks and nearby residues as solid sticks:

fetch 1t3r, async=0
hide everything
show cartoon
create lig, resn 017
show sticks, lig
set stick_transparency, 0.7,lig
show sticks, byres (lig around 5) and not resn 017

Transparent background:

set opaque_background, off

Front-most transparent surface:

set transparency_mode, 2

To render all transparent layers:

set transparency_mode, 1

To increase contrast when rendering:

set ray_transparency_contrast, 1.5

To factor in surface normals:

set ray_transparency_oblique, 1.1

Transparent surfaces not casting a shadow:

set ray_transparency_shadow, 0

No shadows:

set ray_shadow, 0

Transparency in individual molecules:

set stick_transparency, 0.4, molecule4

If drawing multiple selections from Mol4 and want it transparent, for Individual objects:

create M223Dser, /mol4//D/MET`223 and !mc
show sticks, M223Dser
set stick_transparency=0.9, M223Dser

You still have to specify the type of transparency - for sticks - since its not a global object transparency