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@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/m... >
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/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
See also the general page on measurements: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measure... >
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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