[chimerax-users] 答复: calculate volume of voxels

[Tianming Qu]

Thanks for the help Dr. Elaine,

Is there any way I can figure out the coordinates of each voxel?

I know from mdanalysis, if one knows the voxel size (delta) and delta of one voxel cell, the voxel center coordinates can be calculated. Can I do the same way in ChimeraX?

Best,
Tianming


发件人: Elaine Meng <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>
抄送: ChimeraX Users Help <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> 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>
> 日期: 星期三, 2022年9月21日 下午4:10
> 收件人: Tianming Qu <tqu at fsu.edu>
> 抄送: ChimeraX Users Help <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> wrote:
> >
> > Thanks for the so quick reply Dr. Elaine.
> >
> > One more question, can chimera calculate the volume of voxels for density map?
> >
> > Best,
> > Tianming
>
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!PhOWcWs!03B7yr-Dfa3eZffX75Ds2z7GS0qgRXfkjOjkvt6b-NRbZiKRnRPeQrRutR-B_h04w70LE7k-L-mNIA$<https://urldefense.com/v3/__https:/www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!PhOWcWs!03B7yr-Dfa3eZffX75Ds2z7GS0qgRXfkjOjkvt6b-NRbZiKRnRPeQrRutR-B_h04w70LE7k-L-mNIA$>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220922/ec390e63/attachment.html>