[Chimera-users] A question about the Volume Viewer

[Elaine Meng]

Hi Claudio,
The text means that 1% of the 3D space in the volume grid box is inside the isosurface drawn at that level.  You are seeing the whole map, but contoured at this automatically chosen level.  This is just to get something visible/reasonable to start with, and it’s good to hear that it works well in your case, but it’s not necessarily the “best” or most scientifically meaningful level.  Sometimes people adjust the level based on some expected volume per atom, if it’s known what molecules are included in the map.  
I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 9, 2019, at 12:01 PM, Grosman, Claudio F <grosman at illinois.edu> wrote:
>  
> 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.
> Claudio