Robert, thanks for this, changing to the unsigned applet didn't work - I was just trying to avoid duplicating significant amounts of data, but it looks like I don't have a choice here <sigh>
cheers Gemma Robert Hanson wrote: > Gemma, a few things here: > > 1) just one "Jmol.js" script tag, please. > > > jmolApplet(800,"load /ebi/ftp/pub/databases/rcsb/ > > pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz"); > > > > On Tue, Aug 11, 2009 at 5:00 AM, Gemma L. Holliday > <[email protected] <mailto:[email protected]>> wrote: > > Hi, > > I'm new to using Jmol and am having real issues getting it to run > on my website. The html code I'm using is: > > <html> > <head> > <script src="jmol/Jmol.js" type="text/javascript"></script> > </head> > > <body> > <script src="jmol/Jmol.js" > type="text/javascript"></script> > <script type="text/javascript"> > jmolInitialize("jmol"); > jmolApplet(800,"load > > /ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz"); > </script> > </body> > > </html> > > and the web-page is locates at: > http://www.ebi.ac.uk/thornton-srv/databases/MACiE_NEW/test/1b73.html > > the jmol files are located at test/jmol/ > > but all I get is a big grey box... > typing in jmol/jmol.sh runs the application with no error messages... > > I have a moderately long script that I want to run, but I can't > seem to get past the first hurdle. Any help would be gratefully > accepted > > > > Here's what the Java Console says: > > Java Plug-in 1.6.0_12 > Using JRE version 1.6.0_12 Java HotSpot(TM) Client VM > User home directory = C:\Documents and Settings\hansonr > > ---------------------------------------------------- > c: clear console window > f: finalize objects on finalization queue > g: garbage collect > h: display this help message > l: dump classloader list > m: print memory usage > o: trigger logging > q: hide console > r: reload policy configuration > s: dump system and deployment properties > t: dump thread list > v: dump thread stack > x: clear classloader cache > 0-5: set trace level to <n> > ---------------------------------------------------- > > urlImage=jar:http://www.ebi.ac.uk/thornton-srv/databases/MACiE_NEW/test/jmol/JmolApplet0.jar!/jmol75x29x8.gif > > <http://www.ebi.ac.uk/thornton-srv/databases/MACiE_NEW/test/jmol/JmolApplet0.jar%21/jmol75x29x8.gif> > Jmol applet jmolApplet0__208217539741961__ initializing > AppletRegistry.checkIn(jmolApplet0__208217539741961__) > applet context: -applet > appletDocumentBase=http://www.ebi.ac.uk/thornton-srv/databases/MACiE_NEW/test/1b73.html > appletCodeBase=http://www.ebi.ac.uk/thornton-srv/databases/MACiE_NEW/test/jmol/ > (C) 2008 Jmol Development > Jmol Version 11.6.27 2008-11-24 13:39 > java.vendor:Sun Microsystems Inc. > java.version:1.6.0_12 > os.name:Windows XP > memory:4.8/5.2 > useCommandThread: false > appletId:jmolApplet0__208217539741961__ > defaults = "Jmol" > backgroundColor = "black" > language=en_US > > FileManager.openFile(/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz) > > ///ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz > FileManager opening > http://www.ebi.ac.uk/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz > file ERROR: > http://www.ebi.ac.uk/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz > java.io.FileNotFoundException: > http://www.ebi.ac.uk/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz > openFile(/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz): > > 782 ms > eval ERROR: java.io.FileNotFoundException: > http://www.ebi.ac.uk/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz > ----line 1 command 1: > load >> > "/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz" > > << > > > Notice the file name: > > FileManager opening > http://www.ebi.ac.uk/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz > > > Two problems there: 1) using the standard applet you can't access > files outside of the path: > > http://www.ebi.ac.uk/thornton-srv/databases/MACiE_NEW/test/jmol > > (where your Jar file resides). Files can be in subdirectories of that, > but not way out in > > http://www.ebi.ac.uk/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz > > > One way around this is to use the signed applet -- > > > jmolInitialize("jmol", true); > > or > > jmolInitialize("jmol", "JmolAppletSigned.jar"); > > > Another way is to move all the jar files into an upper directory such as > > http://www.ebi.ac.uk/ebi/ftp/pub/databases/rcsb > > > Bob Hanson > > > > > > > All the best > Gemma > > -- > "Even as an instrument of iron or of other metal waxeth soon > rusty unless it be continually occupied, even so shall the wit of > a man or woman wax dull and unapt to do or understand anything > unless it be always occupied upon some manner of study" ~~ Queen > Elizabeth I, 1544 > > Dr Gemma Holliday MChem MRSC > Research Associate > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge > CB10 1SD > Tel: +44 1223 492535 > http://www.docholliday.homecall.co.uk/ > http://www.ebi.ac.uk/thornton-srv/databases/MACiE > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports > 2008 30-Day > trial. Simplify your report design, integration and deployment - > and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > 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 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ------------------------------------------------------------------------ > > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- "Even as an instrument of iron or of other metal waxeth soon rusty unless it be continually occupied, even so shall the wit of a man or woman wax dull and unapt to do or understand anything unless it be always occupied upon some manner of study" Queen Elizabeth I, 1544 *********************************** Dr Gemma L. Holliday MChem MRSC Research Associate EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Tel: +44 1223 492535 *********************************** ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
