[Chimera-users] How to set the contour level correctly?

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 13 12:29:49 PDT 2021

Hi Philipp,
I can't tell if you are talking about electron density like from cryoEM, or a Coulombic electrostatic potential (ESP) map.  Either way, the units shown in the Volume Viewer are not sigma, they are the raw values from the map file.  The "Volume Mean, SD, RMS" tool (or command "measure mapStats") will tell you the mean, standard deviation (SD) from the mean, and the root-mean-square (RMS) deviation from zero but won't affect what is shown in the Volume Viewer.  You'd have to use the stats to back-calculate the contour value that you want, or use command "volume" with "sdLevel" or "rmsLevel" options to do the conversion and set the contour level directly:

If electron density: I don't think there is any universally recommended value.  It depends on the resolution, noise, and other specifics of a given experiment.

If ESP: the Coulombic ESP calculation is mainly for coloring the molecular surface to see relatively positive or negative regions, rather than for display as isopotential contour surfaces.  The values are in kcal/(mol·e) at 298 K.  However, the absolute magnitudes of the values are not that important as you can clearly halve them by doubling the dieletric constant, or double them by halving the dielectric constant, etc.   Thus it is not meant for quantitative calculations, and there is specific recommended contour level for isosurface display.

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

> On Oct 13, 2021, at 11:31 AM, Selenschik, Philipp via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> my apologies if this is a recurring (and potentially trivial) question that does not directly concern Chimeras functionalities.
> I am wondering how to properly set the value of the contour level to visualize a Coulomb potential map.
> When I use the approximation of 1 Da = 1.2 <image003.png>³ to adjust the displayed volume in the Volume viewer dialog almost no secondary structure, but a lot of dust is visible.
> The same problem occurs when I’d like to visualize, for example, an α-helix of a subunit rigid-body fitted to the density. I use the “zone” command to trim the density at a pre-defined 2 Å around the α-helix. 
> But is there any general guideline on how to properly set the contour level? I often find values between 1 σ to 3 σ.
> I assume this is the standard deviation of the map. If so, can it be measured via the “Volume Mean, SD, RMS” command? 
> Kind regards
> Phil

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