[chimerax-users] transition from Chimera

[Tom Goddard]

I fixed ChimeraX opening of files by double clicking a second file on Mac, same fix should also apply to Windows and Linux.  This same fix also makes the shell command on Mac to open a file in the already running ChimeraX work

	% open -a /Applications/ChimeraX.app ~/Downloads/ChimeraX/PDB/1a0m.cif 

and the equivalent on Linux (possibly xdg-open) and Windows (command unknown) should also now work.

This fix will be in tomorrow's ChimeraX release candidate builds.

	Tom


> On May 12, 2020, at 1:36 PM, Guillaume Gaullier <guillaume at gaullier.org> wrote:
> 
> Hi Tom,
> 
> I believe the Linux equivalent of macOS’ "open" is "xdg-open". See https://www.freedesktop.org/wiki/Software/xdg-utils/ <https://www.freedesktop.org/wiki/Software/xdg-utils/>
> 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: https://wiki.archlinux.org/index.php/Default_applications <https://wiki.archlinux.org/index.php/Default_applications>
> 
> Cheers,
> 
> Guillaume
> 
> 
>> On 12 May 2020, at 20:14, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>> 
>> Hi Jerome,
>> 
>>   We don't have the chimerax --send option to open files in an already running ChimeraX, although we plan on adding it.
>> 
>>   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
>> 
>> 	remote rest start port 58123
>> 
>> 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,
>> 
>> 	curl http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/PDB/1a0m <http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/PDB/1a0m>.cif
>> 
>> 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".
>> 
>>   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
>> 
>> 	% open -a /Applications/ChimeraX.app ~/Downloads/ChimeraX/PDB/1a0m.cif 
>> 
>> 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.
>> 
>> 	Tom
>> 
>> 
>>> On May 12, 2020, at 1:50 AM, Jerome Mutterer <jerome.mutterer at ibmp-cnrs.unistra.fr <mailto:jerome.mutterer at ibmp-cnrs.unistra.fr>> wrote:
>>> 
>>> Dear all,
>>> 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 
>>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send>
>>> 
>>> I see that this is not described here:
>>> https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html <https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html>
>>> 
>>> Is that still available somehow in ChimeraX?
>>> Thanks for any input.
>>> Sincerely,
>>> Jerome.
>>> 
>>> -- 
>>> Jerome Mutterer
>>> CNRS - Institut de biologie moléculaire des plantes
>>> 12, rue du Général Zimmer
>>> 67084 Strasbourg Cedex
>>> www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr/>
>>> 
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>> 
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