I am trying to use the following commands in the notebook:
Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only Web application utilizing jQuery, a Java applet, a stand-alone Java program. RuntimeError: jmol cannot run, no suitable java version found Java is installed on this machine, and I think it is working correctly evidenced by the following facts-) I can run 3d plots in the browser using the sage notebook.-) I can install and run jmol via homebrew with no problems. Just when it is started through command line sage, it won't.
but Jmol terminates and just returns a black picture. These commands work fine in the command line. I tried this both on my laptop and on the notebook server at sage.lacim.uqam.ca. Is there some configuration necessary to display jmol pictures in the notebook?
Thanks,
Anne
Comments
Jmol Macros
This is almost certainly to do with your specific configuration. We have had these kinds of issues on a recurring basis. I would suggest searching sage-support (though it's hard to do sometimes) for this. Sometimes it's a Linux thing, sometimes you need to update your Java, and sometimes it's a bug. What version do you have? We did fix some of these things in patches that should be in 4.7.
If you are using Mac OS X + Chrome there is a good thread on sage-support, although that problem was fixed (at least in 4.7.1). You may need to enable your browser to load java applets. Try going to http://jmol.sourceforge.net/demo/alphahelix/ and see if the jmol applet loads.
Jmol Mac Not Working
Thank you for your answers. I am running sage-4.7.1 under Mac OS. The jmol applet loads fine for me when I go to http://jmol.sourceforge.net/demo/alphahelix/ . I am not sure which operating system http://sage.lacim.uqam.ca uses, but the sage version there is sage-4.7. You can get a free account and see whether the problem also occurs for you there.
Thank you for your answers. I am running sage-4.7.1 under Mac OS. The jmol applet loads fine for me when I go to http://jmol.sourceforge.net/demo/alphahelix/ . I am not sure which operating system http://sage.lacim.uqam.ca uses, but the sage version there is sage-4.7. You can get a free account and see whether the problem also occurs for you there.
I am trying to use the following commands in the notebook:
Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only Web application utilizing jQuery, a Java applet, a stand-alone Java program. RuntimeError: jmol cannot run, no suitable java version found Java is installed on this machine, and I think it is working correctly evidenced by the following facts-) I can run 3d plots in the browser using the sage notebook.-) I can install and run jmol via homebrew with no problems. Just when it is started through command line sage, it won't.
but Jmol terminates and just returns a black picture. These commands work fine in the command line. I tried this both on my laptop and on the notebook server at sage.lacim.uqam.ca. Is there some configuration necessary to display jmol pictures in the notebook?
Thanks,
Anne
Comments
Jmol Macros
This is almost certainly to do with your specific configuration. We have had these kinds of issues on a recurring basis. I would suggest searching sage-support (though it's hard to do sometimes) for this. Sometimes it's a Linux thing, sometimes you need to update your Java, and sometimes it's a bug. What version do you have? We did fix some of these things in patches that should be in 4.7.
If you are using Mac OS X + Chrome there is a good thread on sage-support, although that problem was fixed (at least in 4.7.1). You may need to enable your browser to load java applets. Try going to http://jmol.sourceforge.net/demo/alphahelix/ and see if the jmol applet loads.
Jmol Mac Not Working
Thank you for your answers. I am running sage-4.7.1 under Mac OS. The jmol applet loads fine for me when I go to http://jmol.sourceforge.net/demo/alphahelix/ . I am not sure which operating system http://sage.lacim.uqam.ca uses, but the sage version there is sage-4.7. You can get a free account and see whether the problem also occurs for you there.
Thank you for your answers. I am running sage-4.7.1 under Mac OS. The jmol applet loads fine for me when I go to http://jmol.sourceforge.net/demo/alphahelix/ . I am not sure which operating system http://sage.lacim.uqam.ca uses, but the sage version there is sage-4.7. You can get a free account and see whether the problem also occurs for you there.
Jmol For Mac Download
PS: I am using Firefox.
