Hi Brandon, There are at least a couple of parameters to try changing, 3D projection mode and dimTransparentVoxels. E.g. try either/both of the following:
volume all projectionMode 3d vol all dimTransparentVoxels false
See the “solid” volume rendering options and specifically these two settings for explanations. http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#pmode http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimvox
This page about ChimeraX features for working with medical imaging data might also be of interest for anybody who is using the “solid” rendering style (on any type of data): http://rbvi.ucsf.edu/chimerax/docs/user/dicom-quickref.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 15, 2019, at 9:18 AM, Scott, Brandon L. Brandon.Scott@sdsmt.edu 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>
Brandon Scott, PhD SDSMT, Nanoscience <VolumeRotate.mp4>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users