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]> 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
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
>
>
> ------------------------------------------------------------------------------
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>
>
--
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
------------------------------------------------------------------------------
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