<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Yes, ChimeraX modules are importable in user scripts and will work as long as you run the script with ChimeraX.<div><br></div><div>— Zach </div><div><br><div><blockquote type="cite"><div>On Sep 22, 2022, at 08:21, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 12pt; font-family: 宋体;"><span lang="EN-US" style="font-size: 10.5pt; font-family: DengXian;">Also, I notice that there are some python modules in chimerax, can I import them in to my own python code<o:p></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: 宋体;"><span lang="EN-US" style="font-size: 10.5pt; font-family: DengXian;">?<o:p></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: 宋体;"><span lang="EN-US" style="font-size: 10.5pt; font-family: DengXian;"><br>Best,<o:p></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: 宋体;"><span lang="EN-US" style="font-size: 10.5pt; font-family: DengXian;">Tianming<o:p></o:p></span></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm;"><p class="MsoNormal" style="margin: 0cm 0cm 12pt; font-size: 12pt; font-family: 宋体;"><b><span style="">发件人</span></b><b><span lang="EN-US" style="font-family: Calibri, sans-serif;">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;"><span class="Apple-converted-space"> </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" style="color: blue; text-decoration: underline;">meng@cgl.ucsf.edu</a>><br></span><b><span style="">日期</span></b><b><span lang="EN-US" style="font-family: Calibri, sans-serif;">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;"><span class="Apple-converted-space"> </span></span><span style="">星期三</span><span lang="EN-US" style="font-family: Calibri, sans-serif;">, 2022</span><span style="">年</span><span lang="EN-US" style="font-family: Calibri, sans-serif;">9</span><span style="">月</span><span lang="EN-US" style="font-family: Calibri, sans-serif;">21</span><span style="">日</span><span style="font-family: Calibri, sans-serif;"><span class="Apple-converted-space"> </span></span><span style="">下午</span><span lang="EN-US" style="font-family: Calibri, sans-serif;">4:18<br></span><b><span style="">收件人</span></b><b><span lang="EN-US" style="font-family: Calibri, sans-serif;">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;"><span class="Apple-converted-space"> </span>Tianming Qu <<a href="mailto:tqu@fsu.edu" style="color: blue; text-decoration: underline;">tqu@fsu.edu</a>><br></span><b><span style="">抄送</span></b><b><span lang="EN-US" style="font-family: Calibri, sans-serif;">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;"><span class="Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;">chimerax-users@cgl.ucsf.edu</a>><br></span><b><span style="">主题</span></b><b><span lang="EN-US" style="font-family: Calibri, sans-serif;">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;"><span class="Apple-converted-space"> </span>Re: [chimerax-users] calculate volume of voxels<o:p></o:p></span></p></div><div><p class="MsoNormal" style="margin: 0cm 0cm 12pt; font-size: 12pt; font-family: 宋体;"><span lang="EN-US" style="font-size: 11pt;">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 <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>><span class="Apple-converted-space"> </span><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>> <span class="Apple-converted-space"> </span><br>> Best,<br>> Tianming<br>><span class="Apple-converted-space"> </span></span><span style="font-size: 11pt;">发件人<span lang="EN-US">: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" style="color: blue; text-decoration: underline;">meng@cgl.ucsf.edu</a>><br>><span class="Apple-converted-space"> </span></span>日期<span lang="EN-US">:<span class="Apple-converted-space"> </span></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 class="Apple-converted-space"> </span></span>收件人<span lang="EN-US">: Tianming Qu <<a href="mailto:tqu@fsu.edu" style="color: blue; text-decoration: underline;">tqu@fsu.edu</a>><br>><span class="Apple-converted-space"> </span></span>抄送<span lang="EN-US">: ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;">chimerax-users@cgl.ucsf.edu</a>><br>><span class="Apple-converted-space"> </span></span>主题<span lang="EN-US">: calculate volume of voxels<br>><span class="Apple-converted-space"> </span><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>> <<a href="https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapcoords.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z6phcKbZw$" style="color: blue; text-decoration: underline;">https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapcoords.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z6phcKbZw$</a> ><br>><span class="Apple-converted-space"> </span><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>> <<a href="https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z7XwPi_sA$" style="color: blue; text-decoration: underline;">https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z7XwPi_sA$</a> ><br>> <<a href="https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html*volume__;Iw!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z5EkUG-aQ$" style="color: blue; text-decoration: underline;">https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html*volume__;Iw!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z5EkUG-aQ$</a> ><br>><span class="Apple-converted-space"> </span><br>> See also the general page on measurements:<br>> <<a href="https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z4tIITbew$" style="color: blue; text-decoration: underline;">https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html__;!!PhOWcWs!xrqKohxNSCfckLcye7LYBV-K4etN0HWgVHJeRESO5aZvezJihBg0pif9bSakwcYHaNuT_Z4tIITbew$</a> ><br>><span class="Apple-converted-space"> </span><br>> Elaine<br>> -----<br>> Elaine C. Meng, Ph.D. <span class="Apple-converted-space"> </span><br>> UCSF Chimera(X) team<br>> Department of Pharmaceutical Chemistry<br>> University of California, San Francisco<br>><span class="Apple-converted-space"> </span><br>> > On Sep 21, 2022, at 12:18 PM, Tianming Qu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>> ><span class="Apple-converted-space"> </span><br>> > Thanks for the so quick reply Dr. Elaine.<br>> > <span class="Apple-converted-space"> </span><br>> > One more question, can chimera calculate the volume of voxels for density map?<br>> > <span class="Apple-converted-space"> </span><br>> > Best,<br>> > Tianming<br>><span class="Apple-converted-space"> </span><br>> _______________________________________________<br>> ChimeraX-users mailing list<br>><span class="Apple-converted-space"> </span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;">ChimeraX-users@cgl.ucsf.edu</a><br>> Manage subscription:<br>><span class="Apple-converted-space"> </span><a href="https://urldefense.com/v3/__https:/www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!PhOWcWs!03B7yr-Dfa3eZffX75Ds2z7GS0qgRXfkjOjkvt6b-NRbZiKRnRPeQrRutR-B_h04w70LE7k-L-mNIA$" style="color: blue; 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