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 > <craig.sw...@nrel.gov<mailto:craig.sw...@nrel.gov>> 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 > Jmol-users@lists.sourceforge.net<mailto:Jmol-users@lists.sourceforge.net> > 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 > Jmol-users@lists.sourceforge.net > 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
