<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 Tom,<div class=""><br class=""></div><div class="">I believe the Linux equivalent of macOS’ "open" is "xdg-open". See <a href="https://www.freedesktop.org/wiki/Software/xdg-utils/" class="">https://www.freedesktop.org/wiki/Software/xdg-utils/</a></div><div class="">At least it is the most likely to be present on a Linux distribution (it comes with all major desktop environments), but you probably won’t be surprised to learn that there are several different programs doing the same thing, as explained here: <a href="https://wiki.archlinux.org/index.php/Default_applications" class="">https://wiki.archlinux.org/index.php/Default_applications</a></div><div class=""><br class=""></div><div class=""><div class="">Cheers,</div><div class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br class="Apple-interchange-newline">Guillaume</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br class=""></div></div></div></div></div></div><div class=""><br class="webkit-block-placeholder"></div><div><blockquote type="cite" class=""><div class="">On 12 May 2020, at 20:14, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</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 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="">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 type="cite" class=""><div class="">On May 12, 2020, at 1:50 AM, Jerome Mutterer <<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 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="">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="">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" data-smartmail="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 style="text-align: center; font-family: "arial narrow", sans-serif; font-size: 11px;" class=""></div><div style="text-align: left; font-family: "arial narrow", sans-serif; font-size: 11px;" class="">Jerome Mutterer<br class=""></div><div style="text-align:left" class=""><span style="font-size:11px" class=""><font face="arial narrow, sans-serif" class="">CNRS - Institut de biologie moléculaire des plantes</font></span></div><div class=""><span style="border-collapse: separate; font-size: inherit;" class=""><span style="border-collapse:separate" class=""><div class=""><span style="border-collapse:separate" class=""><div class=""><span style="border-collapse:separate" class=""><div class=""><span style="border-collapse:separate" class=""><div class=""><span style="border-collapse:separate" class=""><div class=""><span style="border-collapse:separate" class=""><div class=""><span style="border-collapse:separate" class=""><div class=""><span style="border-collapse:separate;font-size:11px" class=""><div class=""><font face="arial narrow, sans-serif" class=""><div style="text-align:left" class="">12, rue du Général Zimmer<br class=""></div><div style="text-align:left" class=""><span style="border-collapse:separate" class=""></span><span style="white-space:pre-wrap" class=""></span>67084 Strasbourg Cedex</div><div style="text-align:left" class=""><a href="http://www.ibmp.cnrs.fr/" style="color:rgb(17,85,204)" target="_blank" class=""><span style="white-space:pre-wrap" class=""></span>www.ibmp.cnrs.fr</a></div><div style="text-align:left" class=""><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>
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