[Chimera-users] Volume level rms option

Tom Goddard goddard at sonic.net
Thu Jul 30 11:00:13 PDT 2015


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 <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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