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@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@sonic.net> À: "MUTTERER Jerome, IBMP" <jerome.mutterer@ibmp-cnrs.unistra.fr> Cc: chimerax-users@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/PD... <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@ibmp-cnrs.unistra.fr <mailto:jerome.mutterer@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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