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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian">Thanks for the help Dr. Elaine,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian">Is there any way I can figure out the coordinates of each voxel?
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian">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?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian">Tianming<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="color:black">发件人</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"> Elaine
Meng <meng@cgl.ucsf.edu><br>
</span><b><span style="color:black">日期</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">
</span><span style="color:black">星期三</span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">, 2022</span><span style="color:black">年</span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">9</span><span style="color:black">月</span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">21</span><span style="color:black">日</span><span style="font-family:"Calibri",sans-serif;color:black">
</span><span style="color:black">下午</span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">4:18<br>
</span><b><span style="color:black">收件人</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"> Tianming Qu <tqu@fsu.edu><br>
</span><b><span style="color:black">抄送</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
</span><b><span style="color:black">主题</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"> Re: [chimerax-users] calculate volume of voxels<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US" style="font-size:11.0pt">Yes, that is the volume inside the surface, my second suggestion. It depends on the contour level of the surface, of course.<br>
<br>
Elaine<br>
<br>
> On Sep 21, 2022, at 1:15 PM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> 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.<br>
> <image001.png><br>
> <br>
> Best,<br>
> Tianming<br>
> </span><span style="font-size:11.0pt">发件人<span lang="EN-US">: Elaine Meng <meng@cgl.ucsf.edu><br>
> </span>日期<span lang="EN-US">: </span>星期三<span lang="EN-US">, 2022</span>年<span lang="EN-US">9</span>月<span lang="EN-US">21</span>日 下午<span lang="EN-US">4:10<br>
> </span>收件人<span lang="EN-US">: Tianming Qu <tqu@fsu.edu><br>
> </span>抄送<span lang="EN-US">: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
> </span>主题<span lang="EN-US">: calculate volume of voxels<br>
> <br>
> If you mean to just find out the voxel size, you can use command "volume settings" or menu: Tools... Volume Data... Map Coordinates.<br>
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapcoords.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z6phcKbZw$ ><br>
> <br>
> 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.<br>
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z7XwPi_sA$ ><br>
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html*volume__;Iw!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z5EkUG-aQ$ ><br>
> <br>
> See also the general page on measurements:<br>
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z4tIITbew$ ><br>
> <br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D. <br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <br>
> > On Sep 21, 2022, at 12:18 PM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> > <br>
> > Thanks for the so quick reply Dr. Elaine.<br>
> > <br>
> > One more question, can chimera calculate the volume of voxels for density map?<br>
> > <br>
> > Best,<br>
> > Tianming<br>
> <br>
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<o:p></o:p></span></span></p>
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