Re: [PyMOL] Transparent cartoon disapearing with ray trace

[<Mat...@im...>]

pym...@li... wrote on 10/25/2006 08:11:27 PM:

> Hello everybody,
>
> I wish to represent the backbone of my protein in cartoon with a
> transparency of 0.6. Around it I show the surface with a transparency of
> 0.4. (the aim is to highlight some specific residues by showing their
> side chains in stick without transparency).
> I can see the wanted result in OpenGL view. But when I raytrace the
> picture a kind of "Copperfield" effect happens: the cartoon backbone
> disappears (NB: it happens for any kind of combination of transparency
> value for cartoon and surface).
> Is anybody have an idea of what is happening ?
>
> Thanks,
>
> Emeric

Hi Emeric -

Pymol has a few different ways of handling multiple nested transparent
surfaces.  The default is to just show the one closest to the viewer
(uni-layer transparency).  This gives prettier pictures with a single
surface, since you don't see the backside of the protein or any pockets in
the surface.  However, for your purposes, you want multi-layer
transparency.  To select this, choose "Setting->Transparency->Multi-layer".

I just confirmed that this works.  I find the results a bit busy, unless
you're looking at just a small part of the protein.  You may need to hide
background details with the clipping planes.

- Matt


--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
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