[chimerax-users] transition from Chimera

[Tom Goddard]

Hi Jerome,

  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.

	Tom


> On May 15, 2020, at 1:37 AM, MUTTERER Jerome (IBMP) <jerome.mutterer at ibmp-cnrs.unistra.fr> wrote:
> 
> Hi Tom,
> Thank you very much for your answers.
> I didn't try the drag and drop emulation approach, but I confirm the "remotecontrol rest" option at startup works nicely.
> I added the following 2 lines to the Favorites>Settings...>Startup tab
> 
> remote rest start port xxxxx
> open instructions.html
> 
> and it makes it easy to operate.
> Thanks a lot!
> 
> Jerome
> 
> 
> De: "Tom Goddard" <goddard at sonic.net>
> À: "MUTTERER Jerome, IBMP" <jerome.mutterer at ibmp-cnrs.unistra.fr>
> Cc: chimerax-users at cgl.ucsf.edu
> Envoyé: Mardi 12 Mai 2020 20:14:39
> Objet: Re: [chimerax-users] transition from Chimera
> 
> 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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