Hi Mike, The Volume Viewer page is long, so I understand it may be hard to find a specific detail! It’s in the “surface or mesh display” section, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume...> "For surface and mesh displays, each threshold is shown as a vertical bar. Initial thresholds are set automatically. For unsigned data types, an initial threshold is set so that 1% of voxels (1% of the volume encompassed by the data region) lie above it; for signed data types, positive and negative thresholds are placed symmetrically about zero.” I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 19, 2016, at 7:54 AM, MICHAEL POTEAT <mpote001@odu.edu> wrote:
Hello all,
How is the default contour level in the Volume Viewer calculated when you first open up a .mrc file? I've tried the average density, and the root-mean-square of all voxels, but both do not match Volume Viewer's default level. I've tried looking here [http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framev...] for documentation on this, but it does not mention it.
Thanks, Mike