Hi Alexis, Probably I need to word the explanation more clearly, but as I understand it the invert option of “volume zone” only applies to newMap true. Invert specifies whether values in the new map should be zero within the cutoff, or zero beyond the cutoff. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone> When newMap is false, there is no new map within which to set zero values, and instead the surface display is restricted to within the cutoff. Although your expectation is reasonable that “invert” might also work in that case (restrict surface display to beyond the cutoff), it hasn’t been implemented. When newMap is false, it uses the “surface zone” capability, which doesn’t have an invert option. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#zone> So at least for now, “newMap true” if you want the inverted result of density display outside the zone. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2019, at 8:44 PM, Alexis Rohou <a.rohou@gmail.com> wrote:
Hello, I've been playing with volume zone and having good fun, but...
I've noticed that if I set newMap to false, then the invert option is ignored (behavior is as though invert is false, even when I specify invert true).
When newMap is set to true, or not set at all, the invert option has the effect I expected from reading the documentation.
Am I missing something? Hopefully description above is unambiguous but let me know if you need step-by-step. Cheers, Alexis