Thanks to Carsten and Mauricio.
Following approaches work:
1) set stick_transparency, 0.4, molecule4
Useful if you are drawing multiple selections from Mol4 and want it transparent
2) Individual objects
create M223Dser, /mol4//D/MET`223 and !mc
show sticks, M223Dser
set stick_transparency=0.9, M223Dser
Here you still have to specific the type of transparency - for sticks
- since its not a global object transparency, which mesed me up.
Mark,
as far as I know, transparency is supported for sufaces and sticks
or cartoons. Filter the settings menu for transparency to get a
better idea. To set transparency for an object
set transparency = 0.5, <object>
should work
Carsten
Lets say:
pymol> load molecule1.pdb
pymol> load molecule2.pdb
pymol> hide lines
pymol> set sphere_transparency, 0.4, molecule1
pymol> set sphere_transparency, 0, molecule2
pymol> show spheres
Cheers,
Mauricio
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