<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Tianming,<div class=""><br class=""></div><div class=""> It is pretty simple to compute the enclosed volume of a closed triangulated surface. But the ChimeraX code is a bit more complicated because it finds any holes in the surface and tries to cap them off. Here is the Python code for the ChimeraX measure volume command on github</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/surface/src/area.py" class="">https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/surface/src/area.py</a></div><div class=""><br class=""></div><div class="">(it is also distributed with your ChimeraX distribution, e.g. on Mac in ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/surface/area.py). The actual calculation is done in C++ for speed and called from Python and that C++ code is on github here</div><div class=""><br class=""></div><div class=""> <a href="https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/surface/_surface/measure.cpp" class="">https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/surface/_surface/measure.cpp</a></div><div class=""><br class=""></div><div class="">The Chimera Programming Manual has a list of the commands and documentation for the corresponding Python functions. But "measure volume" is not yet documented.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/core/src/commands/user_commands.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/core/src/commands/user_commands.html</a><br class=""><div><br class=""></div><div> Tom</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 6, 2022, at 7:04 AM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><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;" class=""><span lang="EN-US" style="font-size: 10.5pt; font-family: DengXian;" class="">Hi,<span class="Apple-converted-space"> </span><br class="">Thanks for the response.<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: 宋体;" class=""><span lang="EN-US" style="font-size: 10.5pt; font-family: DengXian;" class=""><br class="">One more question, how does the chimeraX calculate out the volume of a density map? I mean, I know how to do this operation through the tools-volume-measure volume, but I am curious what is the source code chimeraX used to calculate this volume.<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: 宋体;" class=""><span lang="EN-US" style="font-size: 10.5pt; font-family: DengXian;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: 宋体;" class=""><span lang="EN-US" style="font-size: 10.5pt; font-family: DengXian;" class="">Best,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: 宋体;" class=""><span lang="EN-US" style="font-size: 10.5pt; font-family: DengXian;" class="">Tianming<o:p class=""></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;" class=""><p class="MsoNormal" style="margin: 0cm 0cm 12pt; font-size: 12pt; font-family: 宋体;"><b class=""><span style="" class="">发件人</span></b><b class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>Elaine Meng <meng@cgl.ucsf.edu><br class=""></span><b class=""><span style="" class="">日期</span></b><b class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span></span><span style="" class="">星期三</span><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">, 2022</span><span style="" class="">年</span><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">10</span><span style="" class="">月</span><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">5</span><span style="" class="">日</span><span style="font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span></span><span style="" class="">上午</span><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">11:37<br class=""></span><b class=""><span style="" class="">收件人</span></b><b class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>Tianming Qu <tqu@fsu.edu><br class=""></span><b class=""><span style="" class="">抄送</span></b><b class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br class=""></span><b class=""><span style="" class="">主题</span></b><b class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">:</span></b><span lang="EN-US" style="font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>Re: [chimerax-users] mrc to pdb<o:p class=""></o:p></span></p></div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 12pt; font-size: 12pt; font-family: 宋体;"><span lang="EN-US" style="font-size: 11pt;" class="">Hi Tianming,<br class="">No -- they are different kinds of data. MRC is a density-map format, PDB is an atomic structure format.<br class="">Best,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <span class="Apple-converted-space"> </span><br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class="">> On Oct 5, 2022, at 6:54 AM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> Hi, is there any way I can convert a .mrc file to .pdb file in chimera?<br class="">><span class="Apple-converted-space"> </span><br class="">> Best,<br class="">> Tianming<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></p></div></div><span style="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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="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;" class=""><span style="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; float: none; display: inline !important;" class="">ChimeraX-users mailing list</span><br style="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;" class=""><span style="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; float: none; display: inline !important;" class="">ChimeraX-users@cgl.ucsf.edu</span><br style="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;" class=""><span style="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; float: none; display: inline !important;" class="">Manage subscription:</span><br style="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;" class=""><span style="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; float: none; display: inline !important;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></div></blockquote></div><br class=""></div></body></html>