<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 Christian,<div class=""><br class=""></div><div class=""> I have fixed this problem in tonight's ChimeraX daily builds. Details are in ChimeraX bug report <a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7491" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7491</a></div><div class=""><br class=""></div><div class=""> ChimeraX normally does not update volume surfaces until they are drawn. The volume is normally drawn after each command you type so this is not a problem. But when you run a series of commands with the --cmd start-up option there is no drawing. A similar situation is when you open a ChimeraX command script file (.cxc suffix). ChimeraX handles script files specially and the volume surface updates immediately without waiting to redraw. I've changed the --cmd option so it runs the commands as if they are a script file.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""> <br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 17, 2022, at 3:54 AM, Christian Tüting 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="">Dear ChimeraX-Team,<br class=""><br class="">I have an issue with the volume measure tool. I would like to measure the volume at different thresholds.<br class="">Using the gui mode, I can type the following:<br class=""><br class="">volume #1 level 1<br class="">measure volume #1<br class="">LOG: Enclosed volume for surface (#1.1) = 4.012e+06<br class=""><br class="">volume #1 level 2<br class="">measure volume #1<br class="">LOG: Enclosed volume for surface (#1.1) = 2.144e+06<br class=""><br class="">So this is functional in principle. But I would like to run this in no gui mode, so the commands are ";" seperated. <br class=""><br class=""><br class="">But, even in gui mode, I got the following:<br class=""><br class="">(threshold was set to 1 before executing)<br class=""><br class="">volume #1 level 1; measure volume #1<br class="">LOG: Enclosed volume for surface (#1.1) = 4.012e+06<br class=""><br class="">volume #1 level 2; measure volume #1<br class="">LOG: Enclosed volume for surface (#1.1) = 4.012e+06<br class=""><br class="">So the threshold level is not applied, prior to the measurement of the volume. <br class=""><br class="">And this is the same in the no-gui mode. I would like to check the volume at 5 different levels, but I got always the same value when executing:<br class=""><br class="">"/usr/libexec/UCSF-ChimeraX-daily/bin/ChimeraX --nogui --cmd 'open cryosparc_P42_J241_002_volume_map_sharp.mrc; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1' --exit"<br class=""><br class=""><br class="">Is there any command, that the threshold level is somehow applied, and the measure volume is executed correctly?<br class=""><br class="">The problem is present in<br class="">UCSF ChimeraX version: 1.4.dev202202240543<br class="">and<br class="">UCSF ChimeraX version: 1.5.dev202207221833<br class=""><br class="">Best<br class="">Christian<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></body></html>