<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="">Oops! I told you it was a hack. :-)<div class=""><br class=""></div><div class="">Above the line</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><i class="">m._report_chain_descriptions(session)</i></div><div class=""><i class=""><br class=""></i></div><div class=""><span style="font-style: normal;" class="">add:</span></div><div class=""><span style="font-style: normal;" class=""><br class=""></span></div><div class=""><span class="Apple-tab-span" style="font-style: normal; white-space: pre;"> </span><i class="">m._set_chain_descriptions(session)</i></div><div class=""><i class=""><br class=""></i></div><div class=""><span style="font-style: normal;" class="">--Eric</span></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 28, 2021, at 2:45 PM, Alexander Julian <<a href="mailto:ajulian@hawk.iit.edu" class="">ajulian@hawk.iit.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-family: tahoma, sans-serif;">I've implemented the code and ran it as you suggested, however the output for the chain description is 'No description available' for each structure.<br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 28, 2021 at 3:48 PM Alexander Julian <<a href="mailto:ajulian@hawk.iit.edu" class="">ajulian@hawk.iit.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class="gmail_default" style="font-family: tahoma, sans-serif;">Thank you so much, Eric!</div><div class="gmail_default" style="font-family: tahoma, sans-serif;"><br class=""></div><div class="gmail_default" style="font-family: tahoma, sans-serif;">I appreciate your help!<br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 28, 2021 at 3:35 PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank" class="">pett@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="">No, as long as you're using --nogui (which it certainly sounds like you should be here) the Log tool will not be started and therefore will have no saved state to restore when the session gets restored. As a hack until that enhancement ticket gets implemented you can force the chain table into the log (after the session is restored) with this code:<div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span><i class="">from chimerax.atomic import Structure</i></div><div class=""><i class=""><span style="white-space:pre-wrap" class=""> </span>for m in session.models:</i></div><div class=""><i class=""><span style="white-space:pre-wrap" class=""> </span>if isinstance(m, Structure):</i></div><div class=""><i class=""><span style="white-space:pre-wrap" class=""> </span>m._report_chain_descriptions(session)</i></div><div class=""><span style="font-style:normal" class=""><br class=""></span></div><div class="">You could put that in a .py file and use 'open' to run it. As an additional hack, you can pretend it's a "preset" and add it to the Presets menu (see Presets→Add A Preset...) so you can easily execute it using that menu.</div><div class=""><br class=""></div><div class="">--Eric<div class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Apr 28, 2021, at 12:56 PM, Alexander Julian <<a href="mailto:ajulian@hawk.iit.edu" target="_blank" class="">ajulian@hawk.iit.edu</a>> wrote:</div><br class=""><div class=""><div dir="auto" class="">I am currently running with --nogui because I'm running an automated process. Would running --offscreen resolve this issue? </div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 28, 2021, 2:54 PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank" class="">pett@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="">Well, whatever the contents of Log tool was when the session was saved should be restored. If there was no Log tool (for instance, if this script creates sessions in "nogui" mode) then nothing is restored.<div class=""><br class=""></div><div class="">--Eric<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Apr 28, 2021, at 12:42 PM, Alexander Julian <<a href="mailto:ajulian@hawk.iit.edu" rel="noreferrer" target="_blank" class="">ajulian@hawk.iit.edu</a>> wrote:</div><br class=""><div class=""><div dir="auto" class="">I am not sure of the exact release version, but it is has definitely been installed this year.<div dir="auto" class=""><br class=""></div><div dir="auto" class="">I create the sessions using a python script and open it with the command line, does that prevent the session messages from restoring? </div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 28, 2021, 1:49 PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" rel="noreferrer" target="_blank" class="">pett@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="">Hi Alexander,<div class=""><span style="white-space:pre-wrap" class=""> </span>There is no command to re-show the chain table. I have added you to the recipient list for the enhancement-request ticket we have open for that.</div><div class=""><span style="white-space:pre-wrap" class=""> </span>Nonetheless, the chain table should still be in the log contents after the session is restored. At least for sessions saved in versions of ChimeraX since March of 2020, when that capability was added. Are you using an old version of ChimeraX?</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>Eric Pettersen</div><div class=""><span style="white-space:pre-wrap" class=""> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Apr 27, 2021, at 3:19 PM, Alexander Julian <<a href="mailto:ajulian@hawk.iit.edu" rel="noreferrer noreferrer" target="_blank" class="">ajulian@hawk.iit.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-family:tahoma,sans-serif">Good afternoon,<br class=""><br class=""></div><div class="gmail_default" style="font-family:tahoma,sans-serif">I was wondering if there was any built-in functionality to show the chain annotations that are shown when the file is first open?</div><div class="gmail_default" style="font-family:tahoma,sans-serif"><br class=""></div><div class="gmail_default" style="font-family:tahoma,sans-serif">When I save a session (.cxs) and reopen it later, this information is missing.<br class=""><br class=""></div><div class="gmail_default" style="font-family:tahoma,sans-serif">Best,</div><div class="gmail_default" style="font-family:tahoma,sans-serif">Alexander<br class=""></div><br class="">-- <br class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><b class=""><font style="background-color:rgb(255,255,255)" face="tahoma,sans-serif" color="#666666" class="">Alexander T. Julian</font></b></div><div class=""><font face="tahoma, sans-serif" color="#666666" class="">PhD Student, Department of Biology, Microbiology</font></div><div class=""><font style="background-color:rgb(255,255,255)" face="tahoma,sans-serif" color="#666666" class="">Bachelor of Science, Biomedical Engineering, <span style="text-align:left;text-transform:none;text-indent:0px;letter-spacing:normal;font-family:tahoma,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none" class="">Cell and Tissue Specialization</span> 2021</font><br class=""></div><div class=""><font style="background-color:rgb(255,255,255)" face="tahoma,sans-serif" color="#666666" class="">Master of Advanced Study, Chemical Engineering 2021</font></div><div class=""><font style="background-color:rgb(255,255,255)" face="tahoma,sans-serif" color="#666666" class="">Illinois Institute of Technology</font></div><div class=""><font style="background-color:rgb(255,255,255)" face="tahoma,sans-serif" color="#666666" class="">Chicago, IL 60616</font></div><div class=""><font style="background-color:rgb(255,255,255)" face="tahoma,sans-serif" color="#666666" class=""><i class="">Phone (727)-735-7104</i></font><br class=""></div></div></div></div></div></div></div></div></div></div>
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