<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Dmitry,<div class=""><br class=""></div><div class="">The volume command has an option to set the surface threshold level to enclose a specified volume. The average volume occupied by a protein is about 1.2 cubic Angstroms per Dalton (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055910/" class="">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055910/</a>). So if I have a 300 KDa complex I could use this command to set the surface threshold level of a cryoEM map</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume #1 encloseVolume 360000</div><div class=""><br class=""></div><div class="">Here is the documentation for this option<br class=""><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/user/commands/volume.html#encloseVolume" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#encloseVolume</a></div><div class=""><br class=""></div><div class="">In general this isn't going to always give the best level because of unresolved domains, extra density such as membranes, noise and low resolution.</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 5, 2022, at 10:53 AM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Dmitry,<br class="">As far as I know, there isn't a command to do it directly. Instead you would need to adjust threshold to reach the target volume as reported by the Measure Volume and Area tool (or perhaps Measure and Color Blobs). The Measure Volume and Area tool will continuously report the volume as you interactively drag the threshold in the Volume Viewer.<br class=""><br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html</a>><br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/measureblobs.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/tools/measureblobs.html</a>><br class=""><br class="">I also don't know the conversion factor between volume and weight, but others on this list may be able to advise if you don't already know the formula.<br class=""><br class="">Best,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D.<br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><blockquote type="cite" class="">On May 5, 2022, at 12:02 AM, Dmitry Semchonok via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Dear colleagues,<br class="">Is there a tool in chimeraX that can set the correct volume threshold level when the Molecular weight of the molecule is known?<br class="">Thank you!<br class="">Kind regards,<br class="">Dmitry<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""><br class=""></div></div></blockquote></div><br class=""></div></div></body></html>