Hi Brandon,
ChimeraX is displaying the volumetric rendering using a stack of xy planes -- when you view the planes edge on you don't see them. You can change this using the volume projection mode.
volume #1 projectionMode 2d-xyz
or
volume #1 projectionMode 3d
The default mode is 2d-z when showing a 3d image that is a thin slab (I think less than 5 to 1 aspect ratio). The 2d-xyz mode will show xy, yz, or xz planes depending on the view angle, and the 3d mode will use planes perpendicular to the view direction.
The reason fo the multiple weird modes is that there are performance and quality tradeoffs, and which is the best mode depends on your data.
Tom
On Mar 15, 2019, at 9:18 AM, Scott, Brandon L. wrote:
I am trying to set the thresholds to properly display volumetric fluorescence data, and for some reason, when viewed from the side, i.e. xz or yz projection, the volume goes black. I've attached two images (top view and side view) with not changes to anything else by positioning, and this can be seen clearly in the rotation video I attached. I guess my question is, is this a bug, or is it acting as it was intended?
Thanks for the help,
-Brandon
<image3.png> <image2.png>
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Brandon Scott, PhD
SDSMT, Nanoscience