I use in one of my scripts the syntax {selected}.size
It fires an error with the very latest Jmol version (it did not previously).
But {* and selected}.size works fine
Same problem and solution with the selector hidden
-Paul
http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html
http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT2.html
Ah, yes, these pages look much better. So what are the results?
The page NT1 should load on all platforms with no issues at all. It is
precisely the stated way of doing things.
Almost every test is currently failing :(
Error: [..\Jmol-datafiles\xyz\zoloft.xyz] java.lang.NullPointerException
org.jmol.adapter.smarter.AtomSetCollectionReader - 326 - initialize
org.jmol.adapter.smarter.AtomSetCollectionReader - 199 - readData
org.jmol.adapter.smarter.SmarterJmolAdapter -
Ok, I got the code right. But it does not work on all browsers. I see no
difference with this code than what I was observing before. Namely, on the
Mac, and the Mac only, and a freshly started mozilla browser (Firefox, Camino,
SeaMonkey), the first structure loads fine, but the
Phil,
I'm just curious about something: On a browser that throws the error
loading chlorophyll, what happens if you execute the following
JavaScript command from the location window (address field) while the
first stucture is displayed in Jmol?
javascript:jmolScript(load
I think I have just diagnosed the problem, but not the solution.
I have opened the java preferences and completely cleared the cache. (I know
Angel, you said that in the first place.) Indeed, firefox loads both
structures as expected and three items now appear in the java cache -- the
applet
And a couple more experiments.
1. If I clear java cache, launch firefox and access the signed applet site
which works fine (and gives the three expected files in the java cache) and
then immediately, without closing Firefox, go to the unsigned applet page, all
works well and the unsigned
If that's the case, Phil, then are you saying that
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm does not work
for you -- when you try to load some other model?
On Sat, Jul 24, 2010 at 5:38 AM, Philip Bays pb...@saintmarys.edu wrote:
Ok, I got the code right. But it does not
you need to report this to Bugzilla.
On Sat, Jul 24, 2010 at 7:09 AM, Philip Bays pb...@saintmarys.edu wrote:
I think I have just diagnosed the problem, but not the solution.
I have opened the java preferences and completely cleared the cache. (I
know Angel, you said that in the first
OK. But first -- I would like someone using a Mac to confirm that they
observe this on the site as well.
On Jul 24, 2010, at 10:12 AM, Robert Hanson wrote:
you need to report this to Bugzilla.
On Sat, Jul 24, 2010 at 7:09 AM, Philip Bays pb...@saintmarys.edu wrote:
I think I have just
also, Phil, you will need to be very specific as to browser version. I'm not
seeing the problem on my Mac with Firefox 3.5.7. But it almost certainly
related to newer security measures that Firefox has installed. Apparently
Java access to its cache is considered local file access and is being
one last thing -- all works properly when you deselect the Java option to
use the cache, right?
On Sat, Jul 24, 2010 at 9:32 AM, Robert Hanson hans...@stolaf.edu wrote:
also, Phil, you will need to be very specific as to browser version. I'm
not seeing the problem on my Mac with Firefox 3.5.7.
Firefox 3.6.8. But it was also an issue in 3.6.7 before .8 was released
yesterday.
But why does it work for you and not for me? Remember, it will work the first
time because it has never cached the page. It is the second and subsequent
times that you start with a new launch of firefox,
On my Mac, OS X 10.6.4:
Safari (5.0) - NT1 works fine. NT2 loads the first structure. Clicking the
button does not produce the chlorophyll structure. The message bar says script
started then immediately says script terminated. The javascript debugger shows
this error: Assertion failed:
Phil and Bob,
With never ending Mac problems of my own, I'm very interested in this
chain. Just so I understand:
1) This a suspected Java cache problem - not a browser cache problem.
Is that correct?
2) Do you know in what default state a Mac user, or Windows user for
that matter, is likely
Sorry Otis and perhaps others. The code on NT2 was left from trying to
reinsert the same structure. It is now updated.
Phil
On Jul 24, 2010, at 11:18 AM, Otis Rothenberger wrote:
Phil and Bob,
With never ending Mac problems of my own, I'm very interested in this
chain. Just so I
On Sat, Jul 24, 2010 at 9:57 AM, Philip Bays pb...@saintmarys.edu wrote:
Firefox 3.6.8. But it was also an issue in 3.6.7 before .8 was released
yesterday.
But why does it work for you and not for me?
Remember, if it doesn't work for you, it doesn't work for some user.
But I didn't
On Sat, Jul 24, 2010 at 10:18 AM, Otis Rothenberger
osrot...@chemagic.comwrote:
Phil and Bob,
With never ending Mac problems of my own, I'm very interested in this
chain. Just so I understand:
1) This a suspected Java cache problem - not a browser cache problem.
Is that correct?
Works fine now on both Safari and Firefox.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 24, 2010, at
yeah -- it happened when I added the associative arrays. This should be OK
now.
On Sat, Jul 24, 2010 at 4:14 AM, Nicolas Vervelle nverve...@gmail.comwrote:
Almost every test is currently failing :(
Error: [..\Jmol-datafiles\xyz\zoloft.xyz] java.lang.NullPointerException
The critical information is the version numbers of the Browsers -- 3.6.7/Mac
is what didn't seem to work.
Phil -- we should also be looking at Java versions.
On Sat, Jul 24, 2010 at 12:22 PM, Jeff Hansen jhan...@depauw.edu wrote:
Works fine now on both Safari and Firefox.
Yes, I just fixed that
On Sat, Jul 24, 2010 at 2:19 AM, Paul Pillot
paul.pil...@ac-orleans-tours.fr wrote:
I use in one of my scripts the syntax {selected}.size
It fires an error with the very latest Jmol version (it did not
previously).
But {* and selected}.size works fine
Same
Jeff: It works on Firefox the initial time you try. If you shut down firefox
and try again, does it work?
On Jul 24, 2010, at 1:22 PM, Jeff Hansen wrote:
Works fine now on both Safari and Firefox.
***
Jeff Hansen
Department of Chemistry
On Sat, Jul 24, 2010 at 2:00 AM, Paul Pillot
paul.pil...@ac-orleans-tours.fr wrote:
I think I will implement a kind of script stacking, that would store
pending scripts while the applet finishes the current script and would fire
the pending scripts in one row, afterwards.
Oh, I wouldn't
I didn't explain myself properly. In fact, the stacking process would issue all
the non-processed script at once in the same script separated by semi-colons,
and maybe by a very short delay to give the illusion of successive scripts.
I haven't tried yet the signed applet with the new 50ms delay,
Just an FYI... I ran across this today:
http://www.molsoft.com/ipad.html
-Tom
Sent from a tiny virtual keyboard.
--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit
I put up a new test page with a series of link to recreate the mouseover
effect. It's at the same URL :
http://librairiedemolecules.education.fr/outils/test/test.htm
My feeling is that it works quite satisfactorily.
The time lapse between each script is 100ms with the useCommandThread directive
Nope. NT1 gives the access denied error. NT2 works fine.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul
Thank you, Nico, for releasing Jmol 12.0.RC27. It's finally time to call
this a version!
This last update adds some very powerful capability to Jmol that various
people have suggested over the years. It feels very much now like we have a
fully functional command language -- almost like bringing
Firefox version? Java version? (Java version can be read from the Jmol popup
menu)
On Sat, Jul 24, 2010 at 3:58 PM, Jeff Hansen jhan...@depauw.edu wrote:
Nope. NT1 gives the access denied error. NT2 works fine.
***
Jeff Hansen
Department of
fun!
On Sat, Jul 24, 2010 at 3:10 PM, Thomas Stout thomasjst...@gmail.comwrote:
Just an FYI... I ran across this today:
http://www.molsoft.com/ipad.html
-Tom
Sent from a tiny virtual keyboard.
--
This SF.net
Firefox version is 3.6.8
Java version is 1.6.0_20
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 24,
No sign of it working on this iPad!
All the best
Nick
Sent from my iPad
On 24 Jul 2010, at 22:16, jmol-users-requ...@lists.sourceforge.net
jmol-users-requ...@lists.sourceforge.net wrote:
Send Jmol-users mailing list submissions to
jmol-users@lists.sourceforge.net
To subscribe or
Sorry all, my finger slipped! Molsoft seemed to want Java or ActiveX neither of
which are an option AFAIK.
All the best
Nick
Sent from my iPad
On 24 Jul 2010, at 22:16, jmol-users-requ...@lists.sourceforge.net
jmol-users-requ...@lists.sourceforge.net wrote:
On Sat, Jul 24, 2010 at 3:10 PM,
Report # 581717
J. Philip Bays
Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
(574) 284-4663
pb...@saintmarys.edu
--
This SF.net email is sponsored by Sprint
What
It's got to be a bad Firefox version.
On Sat, Jul 24, 2010 at 4:14 PM, Jeff Hansen jhan...@depauw.edu wrote:
Firefox version is 3.6.8
Java version is 1.6.0_20
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S.
yeah, anything like
{x}
was broken.
All fixed, both in the version at
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip, Jmol
12.0.RC28_dev
and at SourceForge, that Nico released, Jmol 12.0.RC27
Bob
On Sat, Jul 24, 2010 at 4:14 PM, Paul Pillot
paul.pil...@ac-orleans-tours.fr
Thank you! Somebody's not deleting those files!
On Sat, Jul 24, 2010 at 5:08 PM, Philip Bays pb...@saintmarys.edu wrote:
Report # 581717
J. Philip Bays
Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
(574) 284-4663
Looks like I broke modelKitMode in RC27...
--
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.
--
Bob,
Just testing 12.0.RC28_dev and for my site the DATA command with the
append option (set appendNew true) appears not to work properly (models are
just replaced). Sorry I don't have time to do any more detailed testing. I
didn't have to set the appendNew flag in the past - I think in 11.8
append and set appendNew are two different things -- append means don't
delete the current model; set appendNew means create a new model, don't just
add the atoms to the existing one.
Yes, that's broken in Jmol 12.0.RC27. Just fixed; uploading now.
On Sat, Jul 24, 2010 at 9:54 PM, Dean
By the way, DATA is now merged with LOAD. You basically just use the load
command with all its options (append, filter, {n n n}, unitcell, spacegroup,
etc.) with the data command included in it:
load data append inline
..
end data append inline packed {3 3 3}
Bob
On Sat, Jul 24, 2010 at
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