[Chimera-users] Volume level rms option

[Oliver Clarke]

Great, thanks Tom! Using that command I made an alias which I find useful
for quickly showing a local sphere of map around the center of rotation:

# shows sphere of density of selected radius around center of rotation
# Usage: map_sphere #map_id radius
alias ^map_sphere ac mc; sop zone $1 sel $2; del sel
alias ^map_sphere_off ~sop zone $1

On Thu, Jul 30, 2015 at 2:00 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Oliver,
>
>   The equivalent command for the volume dialog Zone panel is "sop zone”
> (surface operation zone).
>
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sop.html
>
>   Tom
>
> On Jul 30, 2015, at 10:05 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>
> Hi Elaine, thanks, yes I use vop zone a lot for other things, but for this
> particular purpose the Zone feature of Volume viewer would be much better,
> if there were a command to activate it.
>
> Cheers,
> Oliver.
>
> On Jul 30, 2015, at 12:35 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Hi Oliver,
> For the second part of your questions, it’s not exactly the same, but “vop
> zone” will create a new dataset with zero values outside the specified zone:
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> On Jul 30, 2015, at 9:10 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>
> Hi all,
>
> Just a minor usability suggestion - I was wondering if it would be
> possible to add a flag to the ‘volume level’ command that allows the user
> to directly set the map threshold to x*RMS or x*SD?
>
> E.g. volume level rms 5 to set to 5xRMS of the map, using the values
> reported by measure mapstats? At present it is possible to normalize the
> map to rms, which is very handy, but it would be also convenient (for the
> purposes of reporting absolute threshold levels in figure legends etc) to
> be able to set the level as 5*rms but still check the absolute e-/Å^3
> contour that this corresponds to.
>
> Also on a completely different matter, is there any way to access the
> “Zone” feature of Volume viewer from the command line? I would like to
> write an alias that places a dummy atom at the CoFR and displays a
> spherical zone of the selected map (without generating a new map using vop
> zone), but I can’t find the corresponding command line function.
>
> Cheers,
> Oliver.
>
>
>
>
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