[chimerax-users] segmented tomogram density in chimeraX

[Jesse HANSEN]

hi all,


I have segmented a tomogram in Amira and exported to chimera for visualization. I first opened the .rec file in chimera and re-saved as .mrc.  Okay, the segmentation output gives a fully filled volume cube except for the regions of segmentation.   Obviously things are inverted.  Also, the volume viewer shows clear sharp peaks (delta functions) rather than continuous density, as volume slider moves to the right new segmentation features appear.  So I used volume filter with "scale" to -1, and I turned off "displayed subregions only".  This fixed the inversion problem and now as I slide toward the right I see more segmented densities.  However the threshold values are all negative (-250 on the far left to -240 on the far right).   This, combined with the densities being sharp peaks, makes it impossible to use this volume like a regular volume for surface coloring, filtering, segger, etc.  Any suggestion on how to go from this step to a usable density would be appreciated.

thanks!

Jesse

=================================
Dr. Jesse Hansen
Schur Group
Institute of Science and Technology Austria
Am Campus 1
3400 Klosterneuburg
Austria
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