Dear Bob,
apologies for the delay in responding - thanks a lot for your help, the
problem I was having is no more (well, it's morphed into a non Jmol related
one anyway!) and the script now works properly!
All the best
Gemma
2009/8/12 Robert Hanson <[email protected]>
> 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
> _______________________________________________
> 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 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
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