it's the signed applet you want -- I think right now you are using the
unsigned applet. The signed applet should work very well for you. See, for
example, http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot.htm. It
just loads files directly from the RCSB. (or your site!)
AH -- but the real problem is this:
http://www.ebi.ac.uk/ebi/ftp/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz
does not exist. I think what you want there (with the signed applet) is
ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz
My page opens that just fine. Here's another page that you can use to test
the signed applet:
<
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?load%20ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/biounit/coordinates/all/1b73.pdb1.gz
>
I had some problem with that, though, because the ftp connection was too
slow from here. You might inquire about getting an http:// connection to
that database. Might be faster. Or not...
Bob
On Wed, Aug 12, 2009 at 7:49 AM, Gemma L. Holliday <
[email protected]> wrote:
> 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>
> > <
> 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
>
--
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
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