<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="">Thanks a lot<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">El 8 abr 2022, a las 20:44, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> escribió:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Great! Thanks for reporting the problem. I fixed it in Chimera today too. But I encourage everyone to use ChimeraX. Usually we don't do fixes to Chimera anymore unless they are critical, but it only needed a few lines of code changed just like in ChimeraX so I fixed Chimera too.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Apr 8, 2022, at 8:49 AM, Moisés Maestro López <<a href="mailto:mmaestro@cnb.csic.es" class="">mmaestro@cnb.csic.es</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Tom, <div class=""><br class=""></div><div class="">Thanks for the response. I have downloaded the daily build and now it works. </div><div class="">As far as I know the problem also happens in chimera (that is why I had to use my script). </div><div class=""><br class=""></div><div class="">Best regards</div><div class=""><br class=""></div><div class="">Moisés<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">El 7 abr 2022, a las 21:17, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> escribió:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Moisés,<div class=""><br class=""></div><div class=""> That is a bug in ChimeraX. It will be fixed in tomorrow's ChimeraX daily build. Both of the following should work</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume all sdLevel 2<br class=""><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume #1-3 sdLevel 3</div><div class=""><br class=""></div><div class="">but the code processed each volume in turn and due to a bug remembered some of the level parameters from the previous volume.</div><div class=""><br class=""></div><div class=""> Thanks for reporting the problem!</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=""><blockquote type="cite" class=""><div class="">On Apr 7, 2022, at 2:03 AM, Moisés Maestro López 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=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div 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);" class="">volume all sdLevel 2, or </i><i style="caret-color: rgb(0, 0, 0);" class="">volume #1 #2 #3 sdLevel 2</i></div><div class=""><i style="caret-color: rgb(0, 0, 0);" class=""><br class=""></i></div><div class=""><span style="caret-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); font-style: normal;" class=""><br class=""></span></div><div class=""><font 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 class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class=""></span></font></div><div class=""><br class=""></div><div class=""><font 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 class="">alias ^allsd runscript ~/chimeraScriptSD.py</font></div><div class=""><font class=""><br class=""></font></div><div class=""><font class="">allsd 3</font></div><div class=""><br class=""></div></blockquote><div class=""><font 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);" 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 class=""><div class="">import sys</div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font class=""><div class="">import chimera </div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font 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 class=""><div class=""><br class=""></div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font 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 class=""><div class=""><br class=""></div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font class=""><div class="">sdlevel = 2</div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font class=""><div class=""><br class=""></div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font 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 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 class=""><div class=""><br class=""></div></font></div></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font 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 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 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 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></div>_______________________________________________<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=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></body></html>