<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 Yangqi,<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 23, 2021, at 8:34 AM, Yangqi Gu <<a href="mailto:yangqi.gu@yale.edu" class="">yangqi.gu@yale.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Dear Chimera Developer,</div><div class="">I am trying to use an external python script to run some calculations. I am using ChimeraX 1.0 and the script requires the import of mmcif module but apparently it is not installed in ChimeraX 1.0? How should I install this module?</div></div></div></blockquote><div><br class=""></div>The mmcif module is chimerax.mmcif in all versions of ChimeraX. The more pertinent question is why would you need this module explicitly? Wouldn't you just run the "open" command, <i class="">e.g.</i><span style="font-style: normal;" class="">:</span></div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><i class="">from chimerax.core.commands import run</i></div><div><i class=""><span class="Apple-tab-span" style="white-space:pre"> </span>models = run(session, "open /path/to/file.cif")</i></div><div><br class=""></div><div><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="">I also downloaded a newer version 1.1, but it is a precompiled version.</div></div></div></blockquote><div><br class=""></div>1.1 is no more "precompiled" than 1.0 was.</div><div><br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="">Do I need to remove ChimeraX 1.0? Because the older version was installed in /usr/bin with an executable file, but for the newer version, I assume I need to add the path for the executables?</div></div></div></blockquote><div><br class=""></div>Just nuke 1.0. There is no reason to keep it around.<br class=""><br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="">I also need to run some ISODLE refinement with my gpu, will ChimeraX configure gpu automatically?<br class=""></div></div></div></blockquote><div><br class=""></div>AFAIK, ISOLDE will automatically use the GPU for the most part.</div><div><br class=""></div><div><div>--Eric</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div><br class=""></div><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="">Best,</div><div class="">Yangqi<br class=""></div><div class=""><br class="">-- <br class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><br class=""></div>Yangqi Gu<div class="">Graduate Student</div><div class="">Malvankar Lab</div><div class="">Yale University, West Campus</div></div></div></div></div></div></div>
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