volume zone - unexpected behavior when newMap false
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
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
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
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 <help:user/commands/volume.html#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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Great, thanks! Cheers, Alexis On Feb 11, 2019, 10:51 AM -0800, Tom Goddard <goddard@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@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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participants (3)
-
Alexis Rohou -
Elaine Meng -
Tom Goddard