@lists.sourceforge.net
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the results locally before I move content
to server. And I can do it all on an iPad with very little pain.
Otis
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comes to mind immediately.
Sorry if this is old hat, but like I said, this is all new and kind of
wonderful to me.
Otis
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));
}
else {
$('#vmk2')[0].contentWindow.introEcho = echo;
$('#vmk2')[0].contentWindow.loadModel(models2/ethane.txt);
}
});
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On Jul 31
the former (Jmol script) - not the latter
(JavaScript).
Otis
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this. I was just interested in
the various specific reasons.
Thanks again for the response. Your answer to B is particularly helpful.
Otis
Rolf Huehne mailto:rhue...@fli-leibniz.de
July 29, 2014 at 9:37 AM
On 07/28/2014 04:55 PM, Otis Rothenberger wrote:
I'm putting together a presentation, and I
of the
picture.
E) Other
Thanks in advance for any replies...
Otis
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. Constructing a
test post search on the RCSB REST page also produces 0 matches.
It anyone else seeing this problem.
Otis
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https
of error
messages?
I would use
set debugscript
first, then run that and see what it gives.
Bob
On Wed, Jul 9, 2014 at 10:58 PM, Otis Rothenberger osrot...@chemagic.com
wrote:
Bob,
I use the following script to duplicate a model in the Jmol window:
scpt = 'center;var mod2
.
This is not a huge problem. I'm just curious if the renumbering is the
guilty party.
Otis
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();
ev.preventDefault();
On Wed, Jul 2, 2014 at 11:39 AM, Otis Rothenberger osrot...@chemagic.com
wrote:
Bob,
I don't think this one is a cache issue:
On the latest version of JSmol, I can no longer drag/drop/load a model
from a molfile.
Otis
--
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Bob,
I don't think this one is a cache issue:
On the latest version of JSmol, I can no longer drag/drop/load a model from
a molfile.
Otis
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Bob,
Ignore the previous note. The Chrome cache clearing add-on is evidently a
piece of junk! When I went into preferences to clear cache, the problem
disappeared.
Otis
On Sun, Jun 29, 2014 at 4:36 PM, Otis Rothenberger osrot...@chemagic.com
wrote:
Bob,
Safari seems OK, but I'm seeing
Angel and Herman,
I think it's simply:
set unitcell off
Otis
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On Jun 16, 2014, at 2:46 PM, Angel Herráez angel.herr...@uah.es wrote:
Then it must be a typo or a change
When I enter in the console
show showunit?
(meaning
Herman,
There may be a more elegant way to do this, but the following should work:
set unitcell off; draw unitcell MESH NOFILL
The mesh nofill prevents the drawing of the solid unit cell. You may have to
play with colors if you don't want the default.
Otis
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o
Angel,
Set unitcell off takes them both out, at least in JSmol - text and cell.
Per my second note,
set unitcell off; draw unitcell MESH NOFILL
while not elegant should get the job done.
Otis
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On Jun 16, 2014, at 4:00 PM, Angel
an
authoritative answer.
Otis
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On Jun 11, 2014, at 10:08 AM, Robert Hanson hans...@stolaf.edu wrote:
Should I just remove the difference and make InChIKey and InChI both
standard?
On Wed, Jun 11, 2014 at 8:56 AM, Otis Rothenberger osrot
Bob,
Very nice executive summary on the whole issue:
http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html#2.9
Otis
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On Jun 11, 2014, at 10:08 AM, Robert Hanson hans...@stolaf.edu wrote:
Should I just
Thanks Greg,
This is very helpful, especially your ability to test #2. I need to get back to
the ISU folks to let them know that this seems to be working.
Otis
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On Jun 9, 2014, at 4:44 AM, Greg.Black greg.bl...@open.ac.uk wrote
for any assistance.
Otis
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Angel,
In Chrome preferences, there is a checkbox option under downloads:
Ask where to save each file before downloading
If this option is checked, you will be able to name a download file before
saving.
Otis
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On May 27, 2014, at 4
Greg,
If you go to chemagic.com and click the miscellaneous button, the animation
links are at the bottom of the misc control screen. The frames file for this
one is chemagic.com/animations/diels_alderF.TXT
Individual frames are simply molfiles pulled from Jmol. At the time we did
this, we
bonds all around;delay 4;echo;}
delay @{frameInterval};
}
echo The final product is this substituted cyclohexene. ;delay 3;boundbox
{*};centerat boundbox;zoom 0;
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On May 16, 2014, at 10:13 PM, Frieda Reichsman frieda...@mac.com wrote
Bob and Phil,
I see the same thing. Bob, you're getting a 400 error because of an inadvertent
space in your URL:
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound
/name/acetone/SDF?record_type=3d
Note the space after the word compound in your URL above.
Otis
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o
the consequence of convolution? Perhaps I should just use
atomno for my subsequent operations.
Otis
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);
}
After some really weird logic behavior, I finally took a look at this:
alert(Jmol.evaluate(jmolApplet0, ' + key + '.find('SMILES',' + ans + ')
0) == false);
With key and ans as different SMILES, the alert was true.
14.1.12_2014.03.21
Otis
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http
Thanks Bob. It's right there in the docs all marked in green! I just missed it.
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On Apr 21, 2014, at 6:31 PM, Robert Hanson hans...@stolaf.edu wrote:
(Jmol.evaluate can only return String, Integer, or Float values, as was the
case
window, but again that info screen is
so convenient.
Otis
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On Apr 15, 2014, at 1:07 PM, Robert Hanson hans...@stolaf.edu wrote:
You mean what you see with
jmolApplet._showInfo(true)
?
Info.console=none will disable
Bob,
Is there a way to turn off error reporting to the Jmol.setInfo screen?
Otis
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I'm running 14.1.12_2014.3.21 and it's OK Mac Safari, Chrome, and Firefox. This
is OS 10.9.2 Mavericks.
I've been keeping a close eye on iPad, and this version of JSmol runs really
well on iPad Air and iPad 2.
Otis
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On Apr 13, 2014
, it just disappears. Is
anyone else seeing this?
Otis
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flashes on. Shortly after that
a mouse movement makes the model disappear. I'm seeing it on iPad also. Again,
it's random, so it's hard to test.
Otis
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On Apr 12, 2014, at 10:10 PM, Otis Rothenberger osrot...@chemagic.com wrote:
Bob
Bob,
If I do
var x= load filePath
is there a quick way to determine the fileType of the file in x?
I'm trying to make pre-load load script decisions.
Otis
--
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Thanks Bob. It's just that 2 looked weird to me. They both work on iPad and
Android, so I'm a happy camper.
Otis
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On Apr 6, 2014, at 11:23 PM, Robert Hanson hans...@stolaf.edu wrote:
looks great to me
On Sat, Apr 5, 2014
hope on
this several months ago. Android Chrome isn't too shabby either.
Otis
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problem was
evident there also.
I think this was working earlier this week - server problems at some point
along the route?
Otis
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On Mar 21, 2014, at 6:08 PM, Pshemak Maslak n...@psu.edu wrote:
On 3/6/2014 11:23 PM, Robert Hanson
domain issue. After your note, this may well work because I change the response
type before I send it from the server - i.e. unrelated to cross domain.
Otis
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On Mar 7, 2014, at 12:42 PM, Robert Hanson hans...@stolaf.edu wrote:
I could
with SMILES.
Otis
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On Mar 7, 2014, at 3:24 PM, Robert Hanson hans...@stolaf.edu wrote:
Jmol handles this by POSTing the request, not GETting it:
FileManager.getAtomSetCollectionFromFile(http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles
on a direct browser load. I get all this remote stuff
through AJAX and chemagic server scripts, so I'm not sure how long this may
have been an issue.
Mac Chrome is fine, and the subsequent cholesterol MEP speed is good.
Is anyone else seeing this PubChem issue with Safai?
Otis
--
Otis
0.7347967540624076 - - - - 7
H -0.4272906203972308 -0.45489682342005144 -0.9058099170150967 - - - - 8
H -0.7788497796450441 -0.2519180940621916 0.7347994928080308 - - - - 9
end append inline;;
Otis
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On Mar 1, 2014, at 7:15 AM, Angel Herráez
with the multiple
version listings in the console. Here's the two versions by my best
interpretation:
14.0.10_2014.02.19
14.1.11_2014.02.22
Otis
--
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o...@chemagic.com
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On Feb 24, 2014, at 9:14 AM, Ron Mignery remign...@gmail.com wrote:
The problem I saw
to use measure. I'll check
this out again in the morning.
Otis
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On Feb 22, 2014, at 11:16 PM, Robert Hanson hans...@stolaf.edu wrote:
___JmolVersion=14.1.11_2014.02.22
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.11_2014.02.22.zip
Ron,
I may not have played with it enough yet, but I don't see it crashing here:
http://chemistry.illinoisstate.edu/osrothen/JSmolVMK2.htm
Native model kit menu and our model kit script control menu seem ok on Mac
Safari and Chrome. I can't check Windows right now.
Otis
--
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Bob,
I forgot to put in the note last night that you still cannot close the model
kit mode menu once it's opened.
Otis
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On Feb 17, 2014, at 2:20 AM, Otis Rothenberger osrot...@chemagic.com wrote:
Bob,
Our VMK page model edit
a single box checked lead
to uncertain actions.
Otis
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On Feb 17, 2014, at 7:38 AM, Otis Rothenberger osrot...@chemagic.com wrote:
Bob,
I forgot to put in the note last night that you still cannot close the model
kit mode menu
Bob,
I hate to bug you while you're chasing bugs (ouch), but a quick question:
I currently load only JSmol.min.js on page load. Is there any file or files
that could be loaded to immediately cache model kit activity, specifically bond
and atom change?
Otis
--
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o
. This appears to be a menu problem.
Otis
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On Feb 16, 2014, at 10:07 PM, Robert Hanson hans...@stolaf.edu wrote:
Otis, could you try that again? With the release at SourceForge?
This just replaces the file of the same released Friday
window.
Otis
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Sorry Bob. I was focusing on the NMR stuff, which I had on the ISU server. I
had an older version of JSmol on the CheMagic server. It never dawned on me
that model kit stuff might be broken on the new version.
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On Feb 15, 2014, at 5:36
to Resolver. I've asked Markus about this, and he says it makes no
sense to him, but there it is.
Otis
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On Feb 15, 2014, at 7:20 PM, Robert Hanson hans...@stolaf.edu wrote:
just kidding. Much appreciated
Bob,
I think you're partly correct, but that error report is from your page.
Actually, now that I think about it, you may be totally correct! Peter's test
pages are 380X340. That may be more than just a suggestion. My page is tiny.
Your page seems to be 300X300.
Otis
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o
Bob,
Is the following correct in Jspecview hnmr?
1) Double click starts a measurement.
2) Subsequent double click continues a measurement.
3) Single click ends a measurement.
Also, can you clear the screen of measurements?
Otis
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is with JSmol, it's gone in
iPad Air.
Otis
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On Feb 10, 2014, at 3:17 PM, Robert Hanson hans...@stolaf.edu wrote:
Could be.
Measurements are problematic. I'm not happy with the way it is, so feel free
to give suggestions. Probably a set
Oops, I left a word out - problem. Whatever the **problem** is with
Safari/iPad2/JSmol, it's gone on iPad Air. On iPad 2 (after iOS 7), JSmol was
almost useless - painfully slow and frequent Safari crashes. On iPad Air, it's
just fine.
Otis
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http
656)
Otis
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On Feb 9, 2014, at 10:09 PM, Robert Hanson hans...@stolaf.edu wrote:
On Sat, Feb 8, 2014 at 7:36 PM, Otis Rothenberger osrot...@chemagic.com
wrote:
Bob,
Error: Invalid negative value for rect attribute width=-51
:
Error: Invalid negative value for rect attribute width=-51
keep popping up as the page is used. This occurs on your test page also.
Otis
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On Feb 8, 2014, at 1:47 PM, Robert Hanson hans...@stolaf.edu wrote:
What 2D conversion? I
script?
Your
js = Jmol._search;
Jmol._search = function(applet, query) {
unhideJSV();
js(applet, query);
}
seems to do it all - loading and syc. I'm missing something in this that does
the sync.
Otis
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On Feb 6, 2014, at 9:49 AM
is not essential for me going to PubChem. For Resolver calls
involving NIST, I need to do this. I'm not pulling IR and MS spectra from
structured data files. I'm poking around NIST webpages, and the whole process
is pretty nutty. Fortunately, NIST web pages are fairly structured.
Otis
--
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o
it that this means that the 2D to 3D (JME to Jmol) via
Jmol.updateView(false) is not going via Resolver. Is that correct?
Otis
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Bob,
Yeah, from PubChem or ChemSpider.
I don't get it. Is that all that's required - 2D into JSpecView? Or does JSME
need the 2D even though I'm not displaying it?
Otis
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On Feb 6, 2014, at 7:23 AM, Robert Hanson hans...@stolaf.edu
is down. Models in the PubChem database are just
fine for our small model homework exercises.
Otis
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of a proton, ;delay 3;echo;}
if (i == 167){display *;echo regenerates the aromatic ring.;delay 3;}
delay @{frameInterval};
}
echo The final product is 1-chloro-4-methoxy-benzene.;delay 3;boundbox
{*};centerat boundbox;zoom 0;
Otis
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On Feb 2
used as a template. He was doing some hide/show atoms in that previous
animation.
A funny thing happens when non-scripters play with this type of template: They
love it! Tom went into an animation frenzy.
Otis
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On Feb 2, 2014, at 8:51
evaluating frames for display once
the file is loaded in Jmol??? But aside from that, isn't a frame a frame?
Otis
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On Feb 2, 2014, at 10:15 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:
On 2 Feb 2014, at 15:05, Otis Rothenberger osrot
Robert and Robert, et al,
Very, very, very, very nice!
Thanks all
Otis
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On Feb 1, 2014, at 2:54 PM, Robert Hanson hans...@stolaf.edu wrote:
Robert Lancashire and I are happy to announce the first online open-source
fully
, but the basic idea works.
Otis
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On Feb 1, 2014, at 10:56 PM, Otis Rothenberger osrot...@chemagic.com wrote:
Robert and Robert, et al,
Very, very, very, very nice!
Thanks all
Otis
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http
can also do this
with JavaScript by defining an empty unbeforeunload function. I was never sure
if either of these affected supporting files, however. I'm not sure you want to
go this route. JSmol in user cache is a big plus.
Otis
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o...@chemagic.com
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The only thing I can think is that it might be related to one of the page/Jmol
loaded calls that I use:
1) body onload=
2) JSmol ready function
3) JSmol structure loaded callback
Maybe also, server setting related to caching???
Otis
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o...@chemagic.com
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the cookie jar. I did not realize what a pain a broken cookie jar could
be for the user!
Otis
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o...@chemagic.com
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On Jan 28, 2014, at 12:16 PM, Angel Herráez angel.herr...@uah.es wrote:
Hi, Chuck
this is how I see it (but I may not be right
Chuck,
I'm sorry. I misunderstood. I thought you were trying to write Info variable
data to Jmol.setInfo.
Otis
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On Jan 28, 2014, at 12:54 PM, Otis Rothenberger osrot...@chemagic.com wrote:
Chuck and Angle,
I think I'm in basic
is fairly simple molecules.
Otis
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is the big issue for us:
1) With InChI, you can really do some nice searches.
2) With InChIkey, we can do grading of JSME structure and JSmol model questions
on interactive pages.
Not having to interrupt these if Resolver is down is a nice feature.
Otis
--
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o...@chemagic.com
http
- just non-stereo SMILES. There
may have been a recent change in this, but I don't think so.
Otis
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o...@chemagic.com
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On Jan 21, 2014, at 3:13 PM, Philip Bays pb...@saintmarys.edu wrote:
Bob:
As I recall, several years ago you wrote the java applet
Afterthought:
Phil, that's the neat thing about what Bob suggested. It takes unique SMILES
off the table.
Otis
--
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On Jan 21, 2014, at 3:23 PM, Otis Rothenberger osrot...@chemagic.com wrote:
Bob and Phil,
Two responses here
the page until
the script finishes.
3) pop-ups have to be set as ok for the page.
4) The SMILES really needs to be URL escaped.
Pino, Put a model in a JSmol window and run that bottom script from the console
to see what's going on.
Otis
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o...@chemagic.com
http
needed. I had some
problems leaving it out, so I just continued to include it in my pages. If I
have 10 JSmol objects in the body, I do 10 instantiations in the head.
Otis
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On Jan 16, 2014, at 9:00 AM, Kubasik, Matt mkuba
quote
structure in the whole Jmol script.
One thing that made issues go away for me completely is to simply use a
function without an argument. That function, when called, can do anything you
need done after the Jmol script executes.
Otis
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o...@chemagic.com
http
made my problems go away - hence the function with no
argument.
Otis
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On Jan 13, 2014, at 7:36 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il
wrote:
Have you tried it on 14.0.5 with HTML5?
Jaim
On Jan 13, 2014, at 2:26 PM
Jaim,
Quick test on your side: Does alert(1234) work. No quotes - just alert(1234)?
Otis
--
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On Jan 13, 2014, at 7:49 AM, Otis Rothenberger osrot...@chemagic.com wrote:
I'm using 14.0.2. I can check out 14.0.5 later this morning.
I
Rick,
I can help you with #1. The following makes it go away:
script type=text/javascript
Jmol._alertNoBinary = false;
jmolApplet0 = Jmol.getApplet(jmolApplet0, Info);
/script
Otis
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On Jan 10, 2014
this approach before any global site
changes.
Otis
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o...@chemagic.com
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On Jan 10, 2014, at 3:55 PM, Spinney, Richard
rspin...@chemistry.ohio-state.edu wrote:
I can help you with #1. The following makes it go away:
script type=text/javascript
that I didn't know what I was
talking about! I believe Bob has said that there really only is Jmol. I
understand what he's saying with this, but that still leaves some term
confusion.
Otis
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Bob,
I could figure this out by trial and error, but you probably know the answer.
Will JSmol load sdf text files cross domain?
Otis
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OK, Thanks. Are the following observations correct?
Resolver does this.
PubChem does this.
RCSB does not do this.
Otis
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On Dec 30, 2013, at 12:45 PM, Robert Hanson hans...@stolaf.edu wrote:
as long as the server is allowing full
Safari and Firefox sharing the same Java cache???
This doesn't explain the object vs applet thing, however.
Otis
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On Dec 30, 2013, at 4:27 PM, Robert Hanson hans...@stolaf.edu wrote:
It appears that Safari has a very strange feature
Phil,
Exactly. That's what I'm thinking. Safari won't cache it, but it will pull it
from cache.
Otis
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On Dec 30, 2013, at 7:28 PM, J. Philip Bays pb...@saintmarys.edu wrote:
I would think that they both rely on the java console. I
The menu command will bring up the menu, but be careful. The command must be
just menu - no trailing space or CR/LF caused by using [enter] in the
console. The latter will throw an error.
The bad news on an iPad is that the resulting menu does not respond to touches.
Otis
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) stateData = stateData.replace(/#/g, !HASH!);
Since the state variable is used directly in Jmol to RESTORE model state, I now
see why this had to be handled this way. Bottom Line: If you're looking for a
triple bond # in a state file variable, look for %23, not #.
Otis
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o
to a new load seems strange, however.
Otis
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On Dec 9, 2013, at 9:25 PM, Otis Rothenberger osrot...@chemagic.com wrote:
Bob,
With our multi-user feature, I'm attempting to go back to state as the
approach to save/load. I've got
file:
set defaultLattice {NaN NaN NaN};
It is the act of simply loading a model that breaks this line. There in no
pattern - completely random.
This is Mac Chrome with 14.0.1_2013.12.04.
Otis
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and asp.NET scripting, so
maybe it's unique to this configuration.
Otis
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Bob and Phil,
It looks like Resolver is down.
Otis
On Wed, Dec 4, 2013 at 7:34 AM, Philip Bays pb...@saintmarys.edu wrote:
On Dec 4, 2013, at 12:50 AM, Robert Hanson hans...@stolaf.edu wrote:
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.03b.zip
-- local installations
Get
Yikes!
Otis
On Wed, Dec 4, 2013 at 10:34 AM, Robert Hanson hans...@stolaf.edu wrote:
I have sent a note to Markus's former supervisor. (Markus has left NIH).
On Wed, Dec 4, 2013 at 7:41 AM, Otis Rothenberger
osrot...@chemagic.comwrote:
Bob and Phil,
It looks like Resolver is down
for
downloading Safari 7. Perhaps we ought to bail on it for the moment to see
what they are doing in Cupertino. I may drop by the Apple store today and
ask some questions.
Phil
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