[chimerax-users] volume zone - unexpected behavior when newMap false

[Alexis Rohou]

Great, thanks!

Cheers,
Alexis
On Feb 11, 2019, 10:51 AM -0800, Tom Goddard <goddard at sonic.net>, wrote:
> 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 at 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 at 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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>
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