<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="">Good morning, <div class=""><br class=""></div><div class="">I would like to set the threshold of multiple CryoEM Volumes (10-20) at the same time, and I would like to put all of them at the same sdlevel.</div><div class=""><br class=""></div><div class="">I use the command:</div><div class=""><br class=""></div><div class=""><i class="">volume #1 sdLevel 2</i></div><div class=""><i class=""><br class=""></i></div><div class=""><span style="font-style: normal;" class="">But this only work for one volume, if I use </span></div><div class=""><i class=""><br class=""></i></div><div class=""><i style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">volume all sdLevel 2, or </i><i style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">volume #1 #2 #3 sdLevel 2</i></div><div class=""><i style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><br class=""></i></div><div class=""><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-style: normal;" class="">It does not work and the threshold are random. </span></div><div class=""><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-style: normal;" class=""><br class=""></span></div><div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class="">In chimera I had a script that I use for doing that but I have not found the way to do it in ChimeraX. In Chimera, I normally called the script with an alias. </span></font></div><div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class=""></span></font></div><div class=""><br class=""></div><div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class=""></span></font></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class="">alias ^allsd runscript ~/chimeraScriptSD.py</font></div><div class=""><font color="#000000" class=""><br class=""></font></div><div class=""><font color="#000000" class="">allsd 3</font></div><div class=""><br class=""></div></blockquote><div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class="">And the script (chimeraScriptSD.py) was:</span></font></div><div class=""><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><br class=""></span></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class="">import sys</div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class="">import chimera </div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class="">from VolumeViewer import Volume</div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class=""><br class=""></div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class="">mlist = chimera.openModels.list(modelTypes=[Volume])</div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class=""><br class=""></div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class="">sdlevel = 2</div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class=""><br class=""></div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class="">if len(sys.argv)>1:</div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class=""> sdlevel = sys.argv[1] </div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class=""><br class=""></div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class="">for m in mlist:</div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span></div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font color="#000000" class=""><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>chimera.runCommand('volume '+str(m)+' sdlevel '+ str(sdlevel))</div></font></div></blockquote></blockquote><div class=""><font color="#000000" class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class="">But I do not know how to do this in ChimeraX. The key point I do not know how to do is to do a loop that say “for any volume in all the opened volumes”.</div><div class=""><br class=""></div><div class="">Thanks for your help</div><div class=""><br class=""></div><div class="">Moisés</div><div class=""><br class=""></div></font></div><div class=""><br class=""></div><div class=""><br class=""></div></body></html>