listen selection command
Hi, I am trying out a REST listener for selections in Chimera and need help. I can talk to Chimera over REST. I can start an Http listener in Jalview - and verify it in my browser. I have sent this command to Chimera: listen start selection rest http://134.36.162.131:64745/ Then silence. I haven't managed to provoke Chimera into sending me a SelectionChanged notification. I am making selections in the Chimera window - as I can see by the 'Inspect Selection' panel. I have also started Chimera standalone (no REST service) and tried the listen command in the command line, but yet to see any output on a selection. What have I missed or how can I diagnose what I am doing wrong here? Thanks, Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096
Hi Mungo, As for Chimera standalone (notifications sent to stdout rather than a REST service), I experimented a bit. Using the Mac version of Chimera, I opened a structure and changed selections after using the command: listen start selection (A) when I started Chimera by clicking the icon, I’m not sure where the notifications went (I didn’t know where to look for stdout) (B) when I started Chimera from the Terminal prompt as per <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html>, I could see the notifications in that same Terminal window. For example: [chopin:~] meng% /Applications/Chimera1.10.1.app/Contents/MacOS/chimera SelectionChanged: selection changed SelectionChanged: selection changed Thus it is working at some level, although a more complete answer regarding notifications to a REST service may not be forthcoming until our expert on this topic returns to work in a couple of days. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 1, 2015, at 8:43 AM, Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:
Hi,
I am trying out a REST listener for selections in Chimera and need help. I can talk to Chimera over REST. I can start an Http listener in Jalview - and verify it in my browser. I have sent this command to Chimera:
listen start selection rest http://134.36.162.131:64745/
Then silence. I haven't managed to provoke Chimera into sending me a SelectionChanged notification. I am making selections in the Chimera window - as I can see by the 'Inspect Selection' panel.
I have also started Chimera standalone (no REST service) and tried the listen command in the command line, but yet to see any output on a selection.
What have I missed or how can I diagnose what I am doing wrong here?
Thanks, Mungo Carstairs
Can you please try using "listen start selection url http://134.36.162.131:64745/", i.e., use "url" instead of "rest" as the keyword? I think that keyword may have been changed at some point and the code and documentation got out of sync (strictly my fault). Let me know if that does not fix things. Conrad On 5/1/2015 8:43 AM, Mungo Carstairs (Staff) wrote:
Hi,
I am trying out a REST listener for selections in Chimera and need help.
I can talk to Chimera over REST.
I can start an Http listener in Jalview - and verify it in my browser.
I have sent this command to Chimera:
listen start selection rest http://134.36.162.131:64745/
Then silence. I haven't managed to provoke Chimera into sending me a SelectionChanged notification.
I am making selections in the Chimera window - as I can see by the 'Inspect Selection' panel.
I have also started Chimera standalone (no REST service) and tried the listen command in the command line, but yet to see any output on a selection.
What have I missed or how can I diagnose what I am doing wrong here?
Thanks,
Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org <http://www.jalview.org/> www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk/>
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Conrad, I tried changing 'rest' to 'url' but no joy. I've also tried changing the IP address to 'localhost' and to '127.0.0.1' but no better. I also separated out my command "listen start selection rest <url>; listen start models rest <url>" into two separate commands, also no change. Ditto abbreviating 'selection' to 'select'. Like Elaine, I did manage to see the "selection changed" message in a terminal window after starting Chimera that way and issuing the "listen start select" in the command line tool. So still stumped. [By the way, am I right in thinking the 'listen' command won't generate any callback for hovering over an atom to get the popup? Jmol can do this. Probably not needed if we can get the selection notification to work.] Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk ________________________________________ From: Conrad Huang <conrad@cgl.ucsf.edu> Sent: 04 May 2015 18:47 To: Mungo Carstairs (Staff); chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] listen selection command Can you please try using "listen start selection url http://134.36.162.131:64745/", i.e., use "url" instead of "rest" as the keyword? I think that keyword may have been changed at some point and the code and documentation got out of sync (strictly my fault). Let me know if that does not fix things. Conrad On 5/1/2015 8:43 AM, Mungo Carstairs (Staff) wrote:
Hi,
I am trying out a REST listener for selections in Chimera and need help.
I can talk to Chimera over REST.
I can start an Http listener in Jalview - and verify it in my browser.
I have sent this command to Chimera:
listen start selection rest http://134.36.162.131:64745/
Then silence. I haven't managed to provoke Chimera into sending me a SelectionChanged notification.
I am making selections in the Chimera window - as I can see by the 'Inspect Selection' panel.
I have also started Chimera standalone (no REST service) and tried the listen command in the command line, but yet to see any output on a selection.
What have I missed or how can I diagnose what I am doing wrong here?
Thanks,
Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org <http://www.jalview.org/> www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk/>
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
The University of Dundee is a registered Scottish Charity, No: SC015096
Hi Conrad, I think I have goofed over a couple of major details... 1) I was trying to send "listen" command to Chimera before I'd launched Chimera (!) 2) once that was corrected, noticed I had a "list stop selection" command being sent from somewhere else in my code I am now starting to get notifications from Chimera (using 'url' rather than 'rest', as suggested). Thanks for your help, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk ________________________________________ From: Conrad Huang <conrad@cgl.ucsf.edu> Sent: 04 May 2015 18:47 To: Mungo Carstairs (Staff); chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] listen selection command Can you please try using "listen start selection url http://134.36.162.131:64745/", i.e., use "url" instead of "rest" as the keyword? I think that keyword may have been changed at some point and the code and documentation got out of sync (strictly my fault). Let me know if that does not fix things. Conrad On 5/1/2015 8:43 AM, Mungo Carstairs (Staff) wrote:
Hi,
I am trying out a REST listener for selections in Chimera and need help.
I can talk to Chimera over REST.
I can start an Http listener in Jalview - and verify it in my browser.
I have sent this command to Chimera:
listen start selection rest http://134.36.162.131:64745/
Then silence. I haven't managed to provoke Chimera into sending me a SelectionChanged notification.
I am making selections in the Chimera window - as I can see by the 'Inspect Selection' panel.
I have also started Chimera standalone (no REST service) and tried the listen command in the command line, but yet to see any output on a selection.
What have I missed or how can I diagnose what I am doing wrong here?
Thanks,
Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org <http://www.jalview.org/> www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk/>
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
The University of Dundee is a registered Scottish Charity, No: SC015096
Problem now resolved: 1) fixed the rubbish in my code as noted in last post 2) changed 'url' to 'rest' in the "listen start selection" command 3) fixed a configuration issue in Jetty which was causing Http POST to be redirected (to GET) http://stackoverflow.com/questions/17886865/post-request-becomes-get I am now getting the full Chimera POST messages as they should be. Thanks! Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk ________________________________________ From: Mungo Carstairs (Staff) Sent: 05 May 2015 12:37 To: Conrad Huang; chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] listen selection command Hi Conrad, I think I have goofed over a couple of major details... 1) I was trying to send "listen" command to Chimera before I'd launched Chimera (!) 2) once that was corrected, noticed I had a "list stop selection" command being sent from somewhere else in my code I am now starting to get notifications from Chimera (using 'url' rather than 'rest', as suggested). Thanks for your help, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk ________________________________________ From: Conrad Huang <conrad@cgl.ucsf.edu> Sent: 04 May 2015 18:47 To: Mungo Carstairs (Staff); chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] listen selection command Can you please try using "listen start selection url http://134.36.162.131:64745/", i.e., use "url" instead of "rest" as the keyword? I think that keyword may have been changed at some point and the code and documentation got out of sync (strictly my fault). Let me know if that does not fix things. Conrad On 5/1/2015 8:43 AM, Mungo Carstairs (Staff) wrote:
Hi,
I am trying out a REST listener for selections in Chimera and need help.
I can talk to Chimera over REST.
I can start an Http listener in Jalview - and verify it in my browser.
I have sent this command to Chimera:
listen start selection rest http://134.36.162.131:64745/
Then silence. I haven't managed to provoke Chimera into sending me a SelectionChanged notification.
I am making selections in the Chimera window - as I can see by the 'Inspect Selection' panel.
I have also started Chimera standalone (no REST service) and tried the listen command in the command line, but yet to see any output on a selection.
What have I missed or how can I diagnose what I am doing wrong here?
Thanks,
Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org <http://www.jalview.org/> www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk/>
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
The University of Dundee is a registered Scottish Charity, No: SC015096
participants (3)
-
Conrad Huang -
Elaine Meng -
Mungo Carstairs (Staff)