On Sep 22, 2022, at 08:21, Tianming Qu via ChimeraX-users <chimerax-users@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@cgl.ucsf.edu>
日期: 星期三, 2022年9月21日 下午4:18
收件人: Tianming Qu <tqu@fsu.edu>
抄送: ChimeraX Users Help <chimerax-users@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@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@cgl.ucsf.edu>
> 日期: 星期三, 2022年9月21日 下午4:10
> 收件人: Tianming Qu <tqu@fsu.edu>
> 抄送: ChimeraX Users Help <chimerax-users@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@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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