[Chimera-users] Default contour level in Volume Viewer

[Elaine Meng]

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/volumeviewer.html#dispsurf>

"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
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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 at 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/framevolumeviewer.html] for documentation on this, but it does not mention it.  
> 
> Thanks,
> Mike