Re: [PyMOL] transparent electron density silhouette

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

Hi Dan,

I think in PyMOL you can only do this in two steps and compose the two images, e.g. with ImageMagick.

# white background
bg white

# step 1
as surface
set ray_trace_mode, 2
png surface.png, ray=1

# step 2
hide surface
show cartoon
set cartoon_cylindrical_helices
set ray_trace_mode, 1
png cartoon.png, ray=1

# If you have ImageMagick installed
system composite surface.png cartoon.png combined.png
load combined.png

Cheers,
  Thomas


> On Jun 19, 2020, at 4:04 AM, Daniel P Farrell <da...@uw...> wrote:
> 
> Hello,
> I'm working with some cryo-EM density and I'm trying to get my isosurface or volume (whichever's easier) to display transparent except for the curves and turns of the density.
> similar to this (done in chimeraX) https://imgur.com/a/lZuG8gD
> 
> Does anyone know if this is possible?
> 
> thanks
> ~Dan
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.