[PyMOL] How to make Transparency in individual molecules/objects

[Dr. M. M. <ma...@ma...>]

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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