<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 Jerome,<div class=""><br class=""></div><div class=""> Putting that "open instructions,html" in your startup preferences is a nice way to show an HTML interface that could have links that execute commands in ChimeraX. I had not thought of that use.</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><br class=""><blockquote type="cite" class=""><div class="">On May 15, 2020, at 1:37 AM, MUTTERER Jerome (IBMP) <<a href="mailto:jerome.mutterer@ibmp-cnrs.unistra.fr" class="">jerome.mutterer@ibmp-cnrs.unistra.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;" class=""><div class=""><div class="">Hi Tom,</div><div class="">Thank you very much for your answers.</div><div class="">I didn't try the drag and drop emulation approach, but I confirm the "remotecontrol rest" option at startup works nicely.</div><div class="">I added the following 2 lines to the Favorites>Settings...>Startup tab<div style="white-space: pre-wrap; margin: 0px; text-indent: 0px;" class=""><br data-mce-bogus="1" class=""></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px;" class="">remote rest start port xxxxx</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px;" class="">open instructions.html</div></div><div class=""><br class=""></div><div class="">and it makes it easy to operate.</div><div class="">Thanks a lot!</div><div class=""><br data-mce-bogus="1" class=""></div><div class="">Jerome</div><div class=""><br data-mce-bogus="1" class=""></div><div class=""><br class=""></div><hr id="zwchr" data-marker="__DIVIDER__" class=""><div data-marker="__HEADERS__" class=""><b class="">De:<span class="Apple-converted-space"> </span></b>"Tom Goddard" <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class=""><b class="">À:<span class="Apple-converted-space"> </span></b>"MUTTERER Jerome, IBMP" <<a href="mailto:jerome.mutterer@ibmp-cnrs.unistra.fr" class="">jerome.mutterer@ibmp-cnrs.unistra.fr</a>><br class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a><br class=""><b class="">Envoyé:<span class="Apple-converted-space"> </span></b>Mardi 12 Mai 2020 20:14:39<br class=""><b class="">Objet:<span class="Apple-converted-space"> </span></b>Re: [chimerax-users] transition from Chimera<br class=""></div><div class=""><br class=""></div><div data-marker="__QUOTED_TEXT__" class="">Hi Jerome,<div class=""><br class=""></div><div class=""> We don't have the chimerax --send option to open files in an already running ChimeraX, although we plan on adding it.</div><div class=""><br class=""></div><div class=""> I have two ideas for how to do this in current ChimeraX. One is to use the remotecontrol command to tell ChimeraX to accept commands via http. In ChimeraX I enable this with command</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>remote rest start port 58123</div><div class=""><br class=""></div><div class="">Then http requests can run commands in ChimeraX. The http url can be entered in a web browser or from a script. From a script you could use curl or wget programs, for example,</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>curl <a href="http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/PDB/1a0m" class="" target="_blank">http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/PDB/1a0m</a>.cif</div><div class=""><div class=""><br class=""></div><div class="">You could make ChimeraX alway enable http requests by putting the "remote..." command in ChimeraX Settings/Preferences under the Startup tab "Execute these commands at startup".</div><div class=""><br class=""></div><div class=""> The other idea I have is simpler but did not work in my test. ChimeraX accepts files dragged and dropped on the application. On macOS (and probably Linux and Windows) I should be able to run a shell command that says drop this file on ChimeraX. On Mac the shell command looks like</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>% open -a /Applications/ChimeraX.app ~/Downloads/ChimeraX/PDB/1a0m.cif </div><div class=""><br class=""></div><div class="">That worked for starting ChimeraX and showing the first file. But when I run it again to open a different it merely raised ChimeraX and did not open the new file. That is a bug. I've made a bug report for it. I don't know the equivalent commands on Linux and Windows and whether the would work.</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=""><blockquote class=""><div class="">On May 12, 2020, at 1:50 AM, Jerome Mutterer <<a href="mailto:jerome.mutterer@ibmp-cnrs.unistra.fr" class="" target="_blank">jerome.mutterer@ibmp-cnrs.unistra.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Dear all,</div><div class="">I'm trying to transition from Chimera to ChimeraX, but my workflow relies on passing scripts to an open, with GUI, instance of Chimera using --send </div><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send" class="" target="_blank">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send</a><br class=""><div class=""><br class=""></div><div class="">I see that this is not described here:</div><div class=""><a href="https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html" class="" target="_blank">https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html</a></div><div class=""><br class=""></div><div class="">Is that still available somehow in ChimeraX?</div><div class="">Thanks for any input.</div><div class="">Sincerely,</div><div class="">Jerome.</div><div class=""><br class=""></div><div class="">-- <br class=""></div><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="" style="text-align: center; font-family: "arial narrow", sans-serif; font-size: 11px;"></div><div class="" style="text-align: left; font-family: "arial narrow", sans-serif; font-size: 11px;">Jerome Mutterer<br class=""></div><div class="" style="text-align: left;"><span class="" style="font-size: 11px;"><font face="arial narrow, sans-serif" class="">CNRS - Institut de biologie moléculaire des plantes</font></span></div><div class=""><span class="" style="border-collapse: separate; font-size: inherit;"><span class="" style="border-collapse: separate;"><div class=""><span class="" style="border-collapse: separate;"><div class=""><span class="" style="border-collapse: separate;"><div class=""><span class="" style="border-collapse: separate;"><div class=""><span class="" style="border-collapse: separate;"><div class=""><span class="" style="border-collapse: separate;"><div class=""><span class="" style="border-collapse: separate;"><div class=""><span class="" style="border-collapse: separate; font-size: 11px;"><div class=""><font face="arial narrow, sans-serif" class=""><div class="" style="text-align: left;">12, rue du Général Zimmer<br class=""></div><div class="" style="text-align: left;"><span class="" style="border-collapse: separate;"></span><span class="" style="white-space: pre-wrap;"></span>67084 Strasbourg Cedex</div><div class="" style="text-align: left;"><a href="http://www.ibmp.cnrs.fr/" target="_blank" class="" style="color: rgb(17, 85, 204);"><span class="" style="white-space: pre-wrap;"></span>www.ibmp.cnrs.fr</a></div><div class="" style="text-align: left;"><br class=""></div></font></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" target="_blank">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></div></blockquote></div></div></div></div></div></div></blockquote></div><br class=""></div></body></html>