Hi Ben, Sounds like you may want to turn off the "cap high values" option, as described in these previous posts: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002449.html http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-June/002688.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 26, 2008, at 6:56 AM, 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

Hi Elaine and Tom, Thank you for your reply. Unchecking the option indeed solved my problem. Kind regards, Ben On Tue, 2008-08-26 at 09:18 -0700, Tom Goddard wrote:

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:

http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002455.html

Tom

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