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
I see that this is not described here: 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.
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 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/
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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/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/
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@sonic.net mailto:goddard@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/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/
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Guillaume Gaullier -
Jerome Mutterer -
Tom Goddard