[chimerax-users] calculate volume of voxels

[Zach Pearson]

Yes, ChimeraX modules are importable in user scripts and will work as long as you run the script with ChimeraX.

— Zach 

> On Sep 22, 2022, at 08:21, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Also, I notice that there are some python modules in chimerax, can I import them in to my own python code
> ?
> 
> Best,
> Tianming
> 发件人: Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
> 日期: 星期三, 2022年9月21日 下午4:18
> 收件人: Tianming Qu <tqu at fsu.edu <mailto:tqu at fsu.edu>>
> 抄送: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> 主题: Re: [chimerax-users] calculate volume of voxels
> 
> Yes, that is the volume inside the surface, my second suggestion.  It depends on the contour level of the surface, of course.
> 
> Elaine
> 
> > On Sep 21, 2022, at 1:15 PM, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
> > 
> > Not only the voxel map, but also the whole region of the map, for example the colume of the blue region in the following fig.
> > <image001.png>
> >  
> > Best,
> > Tianming
> > 发件人: Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
> > 日期: 星期三, 2022年9月21日 下午4:10
> > 收件人: Tianming Qu <tqu at fsu.edu <mailto:tqu at fsu.edu>>
> > 抄送: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> > 主题: calculate volume of voxels
> > 
> > If you mean to just find out the voxel size, you can use command "volume settings" or menu: Tools... Volume Data... Map Coordinates.
> > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapcoords.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z6phcKbZw$  >
> > 
> > If you mean to measure the volume inside the surface (cubic angstroms) then command "measure volume" or menu: Tools... Volume Data... Measure Volume and Area.
> > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z7XwPi_sA$  >
> > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html*volume__;Iw!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z5EkUG-aQ$  >
> > 
> > See also the general page on measurements:
> > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z4tIITbew$  >
> > 
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.                       
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > 
> > > On Sep 21, 2022, at 12:18 PM, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
> > > 
> > > Thanks for the so quick reply Dr. Elaine.
> > >  
> > > One more question, can chimera calculate the volume of voxels for density map?
> > >  
> > > Best,
> > > Tianming
> > 
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