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

Selenschik, Philipp pselensc at uni-muenster.de
Wed Oct 13 11:31:27 PDT 2021


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 [cid:image003.png at 01D7C06B.AA8F9850] 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

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