[Chimera-users] how is the threshold calculated?

[Elaine Meng]

Hi MS,
>From the Volume Viewer docs (see Display: Surface/Mesh, Solid):
<http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

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.
[...]
For solid displays, each threshold is shown as a small square. Initial thresholds are set automatically. For unsigned data types, initial thresholds are set to give zero intensity for the 10% of voxels (in the data region) with the lowest values, scaling up to 0.99 intensity for the 1% of voxels with the highest values; 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 10, 2010, at 1:12 PM, Mitul Saha wrote:

> Hi!
> In Chimera's Volume viewer, how is the default density threshold computed
> for a given loaded 3D density map?
> Thanks,
> MS