Re: [PyMOL] Pymol Rendering

[Thomas H. <tho...@sc...>]

Hi Seán,

Enabling multi-layer transparency should do the trick.

From the menu:
Setting > Transparency > Multi-Layer

From the command line:
PyMOL> set transparency_mode, 1

Hope that helps.

Cheers,
  Thomas


> On Feb 24, 2020, at 10:32 PM, Seán Downey <dow...@tc...> wrote:
> 
> Hi all, 
> 
> I am trying to render an image of a protein structure with a transparent surface and a slightly less transparent cartoon structure, of the same colour, in order to show both the cartoon structure and a ligand (non-transparent) bound within as well as the surface. Using the ray option, the ligand is visible, but the semi-transparent cartoon is not. Does anyone have any insight into this.  Note I am using version 2.2.3.
> 
> All the best,
> 
> Seán Downey 
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.