[Chimera-users] A question about the Volume Viewer

Grosman, Claudio F grosman at illinois.edu
Fri Aug 9 12:01:57 PDT 2019

Hello everyone,

I have (what I think is) a very simple question: what is the particular value of "level" (that is, the threshold) that appears automatically when one opens a 3D density map? After playing around with the threshold, I always feel like the initial value is the best one, but I wonder what exactly this value is. In the online documentation of Chimera, this issue is addressed. The text reads that the initial value of this threshold is such that 1% of the voxels have density values above it. Is this really the case? Only voxels with intensities above the threshold are displayed. Am I seeing only 1% of the voxels, then?

I am afraid, I am confused.

Thank you very much, in advance.

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