Hi Alexis,

  Some day I will add the code to show inverted volume zones with newMap false.  But for now  I have made it issue an error message saying that combination is not supported.

Tom

volume zone #1 nearAtoms #2 range 5 newMap false invert true

volume zone command currently does not support invert True with newMap False 

On Feb 9, 2019, at 2:01 PM, Alexis Rohou <a.rohou@gmail.com> wrote:

Hi Elaine,

Thanks for the explanation!

I might suggest a warning printed out to the Log when user sets newMap
false and invert true, and/or a tweak to the documentation of "volume
zone" to reflect this.

Cheers,
Alexis

On 2/9/19 1:17 PM, Elaine Meng wrote:

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

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