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 ?
Emeric Wasielewski, Ph. D.
Department of Biochemistry and Molecular Biology
Mayo Clinic College of Medicine
200, First Street SW
Rochester, MN 55905, USA
Office: (507) 284 9189 Fax: (507) 284 1209
pymol-users-bounces@... 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 ?
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.
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
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