[Chimera-users] mrc opaque faces

Tom Goddard goddard at cgl.ucsf.edu
Tue Aug 26 09:18:23 PDT 2008

Hi Ben,

  The opaque volume faces are a feature to improve the appearance when 
objects in the density appear at the edge of the volume box.  For 
inverted maps, ones where objects are low volume values and noise 
regions have high volume values you want to turn off the "cap high 
values at box faces" option as described in a previous post:


Benoit Zuber wrote:
> Hello,
> I have problem looking at maps in mrc format calculated with IMOD. In
> mesh or surface style, when I move "level" towards lower value, the
> outer faces of the volume gradually become opaque. When I set the level
> to the minimum I see a smooth rectangular parallelepiped. I can then
> zoom in and have the camera inside the parallelepiped. With these
> settings, no density is visible inside the parallelepiped, only its
> faces are visible. 
> In 3dmod I checked the edges of the map: they have a variable density,
> and they are not all black, or all white.
> Has anybody got a clue of what's going wrong?
> Thanks
> Ben

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