Forgot one important thing. In my ~/.bashrc script I have: export DISPLAY=:4.0
The solution below won't work without that. Craig On Jan 25, 2011, at 1:22 PM, Swank, Craig wrote: > Ok, I got the Vxrb thing working. I have a python script that imports my > data into a db. At the beginning of the script I start Xvrb in the > background like this: > > from subprocess import Popen, PIPE > vxfb = Popen(['Xvfb', ':4', '-screen', '0', '800x600x24'], stdout = PIPE) > > When the script is finished, I kill the subprocess like this: > > vxfb.terminate() > > Hope that helps all the python people who are out there batch converting cube > files to jvxl files! > > Thanks to the responders. > > Craig > > > > > On Jan 25, 2011, at 1:10 PM, Swank, Craig wrote: > >> Thanks for the suggestion. I tried it and got this: >> >> [cswank@scctest convert_test]$ java -jar >> /app/www/auto_opv/src/opv/opv/views/static/applets/jmol-12.0.19/JmolData.jar >> x.mol -n -s mo.spt >> Exception in thread "main" java.lang.NullPointerException >> at org.jmol.viewer.Viewer.initialize(Unknown Source) >> at org.jmol.viewer.Viewer.<init>(Unknown Source) >> at org.jmol.viewer.Viewer.allocateViewer(Unknown Source) >> at org.jmol.api.JmolViewer.allocateViewer(Unknown Source) >> at org.openscience.jmol.app.JmolData.<init>(Unknown Source) >> at org.openscience.jmol.app.JmolData.main(Unknown Source) >> >> >> I found another thread that suggested using Xvfb, and I'm trying that. I'll >> let you know if I get anywhere. If the JmolData.jar is supposed to work, I >> would much prefer that. >> >> Craig >> >> >> On Jan 25, 2011, at 1:01 PM, Robert Hanson wrote: >> >> No graphics on that Linux. Try JmolData.jar instead of Jmol.jar >> >> On Tue, Jan 25, 2011 at 12:43 PM, Swank, Craig >> <[email protected]<mailto:[email protected]>> wrote: >> Hello, >> I need to convert tens of thousands of cube files to jvxl files. I am able >> to do this on my mac by running a command like: >> >> java -jar Jmol.jar -ionx HOMO.cube script >> >> where script contains: >> >> isosurface SIGN color red blue cutoff 0.02 HOMO.cube; write "myfile.jvxl" >> >> This all works well. The problem is that I need to run this conversion on >> the linux box where I am creating a database with the jvxl files and a bunch >> of other stuff. When I try to do this, I get an error: >> >> java -jar mol.jar -ionx HOMO.cube script >> Exception in thread "main" java.awt.HeadlessException: >> No X11 DISPLAY variable was set, but this program performed an operation >> which requires it. >> at >> java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) >> at java.awt.Window.<init>(Window.java:437) >> at java.awt.Frame.<init>(Frame.java:419) >> at java.awt.Frame.<init>(Frame.java:384) >> at javax.swing.JFrame.<init>(JFrame.java:174) >> at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown >> Source) >> at org.openscience.jmol.app.Jmol.main(Unknown Source) >> >> >> I've seen someone else referencing this same problem on this thread: >> >> https://sourceforge.net/mailarchive/message.php?msg_id=12772213 >> >> So, even with the --nodisplay option set, Jmol needs access to an xserver. >> No x server will be available when my data importer is running. Is there >> any way around this? >> >> Thanks, >> >> Craig >> >> >> ------------------------------------------------------------------------------ >> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! >> Finally, a world-class log management solution at an even better price-free! >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >> February 28th, so secure your free ArcSight Logger TODAY! >> http://p.sf.net/sfu/arcsight-sfd2d >> _______________________________________________ >> Jmol-users mailing list >> [email protected]<mailto:[email protected]> >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> <ATT00001..txt><ATT00002..txt> >> >> >> ------------------------------------------------------------------------------ >> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! >> Finally, a world-class log management solution at an even better price-free! >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >> February 28th, so secure your free ArcSight Logger TODAY! >> http://p.sf.net/sfu/arcsight-sfd2d >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > ------------------------------------------------------------------------------ > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! > Finally, a world-class log management solution at an even better price-free! > Download using promo code Free_Logger_4_Dev2Dev. Offer expires > February 28th, so secure your free ArcSight Logger TODAY! > http://p.sf.net/sfu/arcsight-sfd2d > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
