[Chimera-users] probably a bug

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 16 10:03:15 PST 2016

Hi Michał,
This probably relates also to your previous question.

My best guess is not a bug, but there are several factors to consider:

(1) probably most important, only the left image is isosurfaces at distinct levels, where as the right shows a gradual coloring.  Say you have defined orange as level=1.  In that case the isosurface will only enclose 1 or higher.  However, the gradual color shading will look orange even at lower values as it shades into the next color.  I.e. if in the right image you used white for level=.5, then even values less than 1 but more than .5 will be between orange and white.

(2) step values (subsampling of data) for the isosurface display and surface smoothing settings may also significantly affect the volume enclosed in a contour

(3) the fineness of the triangles (vertex density) of the surface will also affect the spread of coloring in the image on the right

So, getting at your previous question, if you wanted orange only for 1 or higher in the gradual coloring view, you would need to define another color/level immediately below it, say white for 0.9999.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 16, 2016, at 5:21 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl> wrote:

> Hello,
> I visualize density of my data two different way with the same thresholds and observe different sizes of regions. Isn't it a bug?
> --
> pozdrawiam serdecznie
> Michał Kadlof <m.kadlof at cent.uw.edu.pl>
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