to download Java 7 for Mac OS X (10.7.3 and
above).
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Sep 4, 2012, at 2:39 PM, Rzepa Henry wrote:
>
> On 4 Sep 2012, at 19:18, Oliver Stueker
> wrote:
>
>> Hi,
>>
>> the security issues with Java 1.
Bob,
Are Jmol SMILES internally unique?
Otis
--
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o...@chemagic.com
http://chemagic.com
--
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t
Angel,
Bingo! That works.
Thanks
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jul 13, 2012, at 2:51 PM, Angel Herráez wrote:
> Otis,
>
> maybe { model=i }
> ?
>
> e.g. this works:
> print {m
}.atomIndex.max + 1;t = {1.2}.atomIndex.min;select within(branch,
{atomIndex = k}, {atomIndex=t}); hide selected
But I don't know how to incorporate the frame index i into the expression.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagi
.
Bob, thanks for the helpful suggestions on this.
Otis
--
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o...@chemagic.com
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Bob,
On our end, this all started with a request from one of Tom's
colleagues. He's using the VMK in a service outreach lecture series to
discuss, among other things, how chemists know what molecules "look
like." We thought it would be neat to be able to discuss this with a
series of edited m
Also, there are only 16,000 compounds there for IR. We could almost
just catalog them. Maybe Markus can add them to the Resolver.
Do you need an introduction?
Bob
On Tue, Jul 3, 2012 at 2:07 PM, Otis Rothenberger
mailto:osrot...@chemagic.com>> wrote:
Bob,
Almost, but not qui
except for the
spectrum index= query.
At first, I though I could go directly to NIST with the InChI to parse the CAS
#. Unfortunately, such a query often returns an intervening options page that
has no CAS numbers.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jul 3,
1 to 0 (or
other integer!) if you get a NO DATA screen for a compound where NIST actually
does have spectrum.
Still a lot of work, but this is doable.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
--
Just to close this issue:
I waited a few days to make sure the problem was fixed. It seems it was a proxy
server issue. I changed the FIrefox default of from "auto detect" proxy to "no
proxy," and this seems to have solved the problem.
Thanks again...
Otis
--
exclusively and only use other
browsers to check my scripting. I'll change the FF default on DNS prefetching
to see if this solves the problem.
Thanks again...
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jun 28, 2012, at 1:03 PM, Otis Rothenberger wrote:
> All-
>
l get appropriate addresses and give this a try. The main importance of your
feedback is that it shows that this is not a Resolver issue. It has to be a
local issue. Thanks again for the feedback.
Markus, thanks for looking into this.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagi
Jeff,
I'm reading the Resolver files as http, and I'm not messing with the headers.
It never bothered me because the load works, but maybe that's part of the
problem. Markus?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jun 28, 2012, at 8:32 AM, Je
AJAX from my server. Did I understand Bob correctly? Is it
theoretically possible to hit Resolver directly via the JmolScript?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jun 28, 2012, at 9:07 AM, Paul Pillot wrote:
> Tried it twice today (morning and afternoon):
&
Cl%29CC
Jim (cc'd with this note), would you forward this note to the ISU chemistry
faculty list?
Thanks in advance for any help. You'll either get the sdf of (R)-2-chlorobutane
or you'll timeout.
Otis
--
Otis Rothenberger
o...
ed for what I need. The focus() by itself does not work. It
needed to be preceded by the blur(). The final blur() is inserted so subsequent
key pressing does not mess up my field contents. The net result is that after
an atom click, key capture is returned to the page.
Otis
--
Otis Rothenberge
reinitiate the page keystroke capture.
Clicking the page itself does not reinitiate the capture.
I suspect that this is a general applet issue. Is there any way within
JmolScript to reinitiate this page JavaScript behavior?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://ch
78205} {3.8535705 3.2247012
3.131318}
Using surface reader org.jmol.jvxl.readers.AtomPropertyMapper@34e67d
14 atoms will be used in the surface calculation
0 contour lines; separation = 0.14
isosurface1 created with cutoff=0.0; isosurface count: 1
isosurface full data range -0.08323054 to 0.08682171
Bob,
I'm in Tampa right now.I have the entire console report at home, and I'll
send it when I get back to Anna Maria Island. For what it's worth now, I'm
pretty sure that I was repeatedly clicking the Load ethane link on the VMK
Edit screen. I noticed the hang up when I clicked the MEP 100 link
riptQueueRunnable.runScript(Unknown
Source)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
Source)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
--
Otis Rothenberger
o...@chemagic.com
http://c
Rolf,
I didn't even have Java debugging turned on. I thought it was on by default. I
have it on now. Thanks for the suggestion.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jun 21, 2012, at 11:24 AM, Rolf Huehne wrote:
> On 06/21/2012 03:43 PM, Otis Roth
s is not a Jmol problem. Things that cause this fatigue
have worked numerous times prior to the onset of a fatigue incident. I cannot
raise the Jmol console to look at history, however.
Does this sound like a Java memory issue? Does anyone else have experience with
"applet fatigue?"
Oti
d, multiple CSIDs will be returned. This latter point is
actually of some use in partial structure/name searches.
Otis
--
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o...@chemagic.com
http://chemagic.com
--
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Bob,
That fixes the arrow problem. Thanks
Otis
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Bob,
Lines (and curves) are draggable and arrows are not. Is this a correct
observation? I am seeing that while arrows do not actually move, the new arrow
position resulting from a drag attempt is reported in the console. Again is
this correct?
Otis
--
Otis Rothenberger
o...@chemagic.com
on the virtual model kit to make either XeHHYY, the
resulting SMILES does not reflect stereochemisty. If, however, you do the same
thing with deuterium, the stereochemisry IS reflected in the SMILES.
Bug or inherent behavior of H replace in modelkitmode?
Otis
--
Otis Rothenberger
o
Yikes! The pond is full of ducks.
Thanks all. There clearly is an eval function in jmolScript.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 17, 2012, at 2:53 PM, Robert Hanson wrote:
> also
>
> x = script(".")
>
> returns the out
Paul,
Your first suggestion worked just fine. This one, however, is cleaner - no
applet name required.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 17, 2012, at 2:20 PM, Paul Pillot wrote:
> Too quick ! The following is even better for your purpose :
>
Paul,
It doesn't look like an eval function, but it sure quacks like one. It's an
eval function!
That does the job for me. Thanks.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 17, 2012, at 2:16 PM, Paul Pillot wrote:
> Have you tried this approa
Angel,
No. I was looking for a jmolScript equivalent to the JavaScript eval()
function. I can work around my current problem if this is not an option, but I
thought I'd check before I go the alternate route.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 17,
Bob,
Is there a way to execute JmolScript that is in a string variable - i.e. an
eval function approach?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
--
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Exclusive
Thank you Paul. Your approach is certainly cleaner. If you're wondering what
var z="" is all about, I don't have a clue. It's obviously a remnant of a lot
of trial an error fumbling around to find out why the zero charges were not
being mapped.
Otis
--
Otis Rothenberg
ll of this in my attempt to set up dynamic MEP. I hope to have
it all set up and fixed this week end.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 12, 2012, at 3:54 AM, Paul Pillot wrote:
> Otis,
> I think the green surface is great and I was just wonde
w the green surface that
suggests close to non-polar bonding. I broke this trap when I was adding the
dynamic MEP feature. Thanks for picking up on this.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 11, 2012, at 10:47 AM, Pillot Paul wrote:
>> I've play
Bob,
That fixes it. Thanks.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 11, 2012, at 12:08 AM, Robert Hanson wrote:
> Sorry -- two steps forward, one back.
>
> Should be OK now. http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>
>
Bob,
I think it's still broken. If you build by hydrogen replacement, minimize
works. When you build by making C-C or C-AnyAtom, minimize breaks.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 10, 2012, at 7:02 PM, Robert Hanson wrote:
> found it. Sorry ab
Bob,
Minimize may still be broken. By way of example, if ethane is appended ethane
(same frame) and then connected to form butane, minimize seems to break.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
Bob,
It is very cool. I have is set up at:
http://chemagic.com/web_molecules/script_page_large.aspx
On the edit screen, if you click mepOn, then subsequent edits are automatically
re-maped. The clear link turns this off. It's actually hard to stop playing
with it.
Otis
--
Otis Rothenb
far as Jmol is concerned.
On an unrelated 12.3.24 issue, was the partial single bond extraction bug fixed
on this version?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 8, 2012, at 4:04 PM, Robert Hanson wrote:
> OK, this is working.
>
> http://chemapp
Very impressive!
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 8, 2012, at 4:04 PM, Robert Hanson wrote:
> OK, this is working.
>
> http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm
>
> load a model by name from either PubChem or NCI
>
Wow!
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 7, 2012, at 6:52 PM, Robert Hanson wrote:
> Jmol 12.3.24 will calculate charges using the MMFF94 model. Thus, you will be
> able to do this:
>
> load caffeine.xyz
> calculate partialcharge
> isos
Thanks on the partial bond bug fix Bob.
I dealt with the other issue with some scripted model nudge links.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On May 3, 2012, at 2:18 PM, Robert Hanson wrote:
>
>
> On Thu, May 3, 2012 at 9:41 AM, Otis Rothenberger
good. If a model is
edited to introduce a partial single bond, then the subsequent molfile
extraction does NOT show this bond as a type 8. Is that a simple fix or a new
feature request?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
Angel and Keith,
I don't know if this is relevant.
Bob did implement this for the ESP charges in Spartan files. There is a filter
ESPCHARGES command that needs to be used to load the ESP charges into Jmol
partial charges. Might this be the case for your files?
Otis
--
Otis Rothenber
Keith,
I think the following should work:
color {*} partialCharge;color label yellow;label %-8.4[partialcharge]
The obscure -8.4 sets rounding. The following will illustrate this point:
color {*} partialCharge;color label yellow;label %[partialcharge]
Otis
--
Otis Rothenberger
o
Bob,
This works now on my Mac Firefox.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Apr 24, 2012, at 10:49 AM, Robert Hanson wrote:
> the :smiles:C/C=C/C business was indeed my forgetting to upload the latest
> JAR files.
>
> http://chemapps.sto
Bob,
I just cleared cache on Firefox Mac, and now the only "direct database calls -
no server" error I still see is:
load :smiles:CC/C=C/CC (PubChem SMILES)
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Apr 24, 2012, at 9:44 AM, Robert Hanson wrote:
>
curiosity, how are you going after that PubChem SMILES load?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
> Dear Jmol users,
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> Needs testing on iP
Bob,
I'm not sure because I didn't know you could do that! Do you mean I don't have
to use a server readURL script on my server to query Resolver. I can simply
query Resolver directly via an AJAX script?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On A
rges, still the MEP's still have some classroom utility
in my opinion. I assume PubChem's abbreviated partial charges are rooted in
making charge profile searches practical.
Bob added the Jmol reading of these PubChem partial charges in 2010, I think.
Otis
--
Otis Rothenberg
side script (my server) that loads a Resolver (or
PubChem/ChemSpider) SDF file?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote:
> Otis, forget that. Don't go there. Period. This is just what we are setting
> up now,
ne throws an obscure JS error - TypeError: h is undefined.
If I directly copy the returned AJAX text and paste it into a direct definition
of lsdfStr, the dynamic load works.
Any thoughts would be appreciated.
Otis
--
Otis Rothenberger
o...@chemagic.com
Bob,
Re iPad: Wow.
It's going to take me some time to figure this all out. Very nice.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Apr 12, 2012, at 6:39 PM, Robert Hanson wrote:
> Paul, first, check this out now:
>
> http://chemapps.stolaf.edu/jmol/ch
and that may be too optimistic.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Apr 3, 2012, at 2:55 AM, Rzepa Henry wrote:
>
> On 3 Apr 2012, at 05:20, Jeff Hansen wrote:
>
>> Assuming everyone wants to spend $20 for a Windows only application I
>> s
Jeff and Bob,
Oops, I forgot that AccuTrans 3D was a Windows only application.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Apr 3, 2012, at 12:20 AM, Jeff Hansen wrote:
> Assuming everyone wants to spend $20 for a Windows only application I suppose
> you mi
ss. If the quality is satisfactory to users,
the AccuTrans 3D batch process makes me think that you don't need to put
Collada translation at the top of your todo list.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Apr 2, 2012, at 10:35 PM, Robert Hanson wrote:
>
these animations. We welcome and
will credit any animation contributions.
Be forewarned. Tom is ahead of me on this. I still have considerable interface
work to do, but what exists now is usable.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagi
ipulatable model for iPad.
This use of AccuTrans 3D is MUCH better than the more convoluted approach I
posted previously.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
>
>
> a) For fixed textbook like presentations, views can be packaged as .pngs or
> animat
Bob,
Thanks. This will not be a problem. I just wanted to know which direction to
take.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Mar 28, 2012, at 10:45 AM, Robert Hanson wrote:
> yes, that is correct. very important from a design issue.
>
> On Tue, Mar
Bob,
I'm working on a model kit mode frames animation creator/editor. On the frame
editing side, it appears that model kit mode will only allow editing of the
last frame. Am I correct on this observation?
If so, is this by design or possibly by code necessity?
Otis
--
Otis Rothenber
vwd = declaration. I arrived at
this by more trial and error than I care to remember.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Mar 11, 2012, at 4:45 PM, Robert Hanson wrote:
> examples?
>
> 2012/3/11 Angel Herráez
> Dear users
> I'd
a problem.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Feb 7, 2012, at 8:16 AM, Robert Hanson wrote:
> Hmm. So that's only minimally operational. Still, it will be interesting to
> see what it all looks like.
>
> On Mon, Feb 6, 2012 at 11:12 PM, Otis Rothenb
ng on. The models also have triangulated surfaces. For what I'm
doing, neither of these issues present a problem.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Feb 6, 2012, at 1:48 PM, Robert Hanson wrote:
> I think I could write a Collada export fairly quickly. I h
r the small models that I'm using.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
--
Try before you buy = See our experts in action!
The most comprehensive online learning library for Microso
amp;list=PLB27087C529DD2120&lf=plcp
If you want more specific information about setting this up after seeing the
video, let me know.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jan 12, 2012, at 6:06 PM, r...@ellerbach.com wrote:
> On Thu, January 12, 2012 4:29 pm, FyD wro
http://www.youtube.com/watch?v=x7f3BAqfzDM
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jan 2, 2012, at 9:26 PM, Eric Martz wrote:
> If someone has experience generating true movies from Jmol (movies
> that will play in a web browser, or at least will play on both
P for most simple models. I
should also mention that not all PubChem files have partial charges.
We're still looking for an alternative, but we haven't found it yet.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 30, 2011, at 1:41 PM, Robert Hanson wrote:
>
SMILES, Jmol can
mediate the above translation. If you want to see this in action, go to:
http://chemagic.com/web_molecules/script_page_large.aspx
Click "The Molecular Editor" Then "Image." The "NIH 2D Capture" link
will illustrate the Jmol mediated transla
but don't
forget that Resolver will do a SMILES ---> to JME file translation.
Otis
Otis Rothenberger
chemagic.com
On 7/26/2011 2:23 PM, Angel Herráez wrote:
> (Sorry, I'm away on holidsya and can't follow this as closely as I would like)
>
> Paul, I think that all
olved the
problem.
Otis
Otis Rothenberger
chemagic.com
--
Magic Quadrant for Content-Aware Data Loss Prevention
Research study explores the data loss prevention market. Includes in-depth
analysis on the changes wit
x27;s good you reported it again.
Otis
Otis Rothenberger
chemagic.com
On 7/25/2011 4:30 PM, Paul Pillot wrote:
> After further testing, at Angel Herraez DIY pages :
> http://biomodel.uah.es/en/DIY/ ...
> I tried all the different sketchers, and they all give the same result with
> t
ith C, you will see the problem.
Correct hydrogens also has a related problem.
Otis
--
Otis Rothenberger
chemagic.com
--
AppSumo Presents a FREE Video for the SourceForge Community by Eric
Ries, the creator of the
turns out that ChemSpider has already used Jmol
to provide a URL that may be of interest to the Wikipedia group:
http://www.chemspider.com/ImageView.aspx?mode=3d&id=9041149
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal,
Marvin.
Finally, the following ChemSpider page contains specific information about
what's behind some of the CheMagic url's above:
http://www.chemspider.com/InChI.asmx
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State
Oh my,
MSIE 9: F12 then script tab
All the immediate JavaScript control you want, I'm impressed.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
From: "Otis Ro
-down.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
From: "Robert Hanson"
Sent: Monday, May 30, 2011 12:10 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol
p://chemagic.com/aka/
Comments and suggestions would be welcome.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
--
vRanger cuts backup time in h
problem in your page. I
see that you have a number of on mouse event trappings on the page. Is it
possible that the applet container inherited something unintended?
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
have to overlap them. It (0,0 where there is a slight
overlap) was just a convenient place to stick JME until the div was made
visible by the user.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
--
emulate meta tag that you
suggested, I can ignore MSIE 9 issues. I can never remember how to type
emoticons, but place a very big smile here.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----
probably solve the div tag style issue.
I did not know about MSIE compatibility tag. I have to check into that. It
would be a wonderful way the tell MSIE to go stand in the corner until I have
time to deal with you - back to shoe lace washing again!
Thanks for the suggestions, Otis
--
Otis Ro
that I did not lose the translucent style. This is
supported by all "modern" browsers, but it's not "legal." I guess I'm going
to lose "legal" new styles by lowering the bar, but "illegal" new styles
will slip under the bar.
Otis
--
Oti
tag I use
for JME in the page. Setting the bar lower looks like a good plan for now.
Angel, I just thought of something. That yellow applet message could have
come from JME. It's sitting right there. It's just hidden!
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois Stat
Bob,
That's interesting! What the heck is going on?
Suddenly, I'm not interested in washing my shoe laces any more.
OR
Did our emails cross? I just changed the doc type. Did your test use this
new document?
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State
h its Errors (RED), Warnings
(Yellow), Messages (Blue) system, so finding the error is not going to
involve the obvious. For future reference, I'll let you know if I find it.
Thanks again for the help.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal
ssion. Consequently, finding the error manually is probably going
to be a quest!
I'll try stepping back from that page header first to see if that works.
That may be what "compatibility mode" is doing any way.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State U
ike the idea of giving up localhost development, but I may have to do
that.
On the other hand, it's that page - not Jmol in general. There is something on
that page that MSIE 9 does not like.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 6
without taking the system down or the browser down it simply tells you the
page would crash the browser.
Thanks for any help or advice.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal,
n, I tried liberalizing Windows security settings
on the localhost Web site - i.e. anybody can do any thing! No luck, Java higher
than than 1.6.0_21 will not allow an applet to read a file via the localhost
server.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
va update makes your problem go away.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
From: "Jay Vyas"
Sent: Friday, May 06, 2011 11:56 PM
To: jmol-users@lists.sourceforge.ne
Paul,
I see the same thing. If I gently rotate a fragment, I can see that it's
translating as I rotate it. No matter which way I rotate, the translation is
always in the same direction - toward infinity. As you say, this behavior is
initiated by the rotate compare command.
Otis
--
deep space!
I assume that that initial hover or click (not sure which) is
selecting the connected branch (model in this case) for rotation. I
never saw this as a bug, but maybe it is.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http
long time MS product user, I must
admit that MS can be trying at times.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
From: "Berger, Daniel"
Sent: Friday, April 29
Bob,
I'm pretty sure ChemSpider is an algorithm for SMILES to InChI. The the
PubChem issues, however, are real. A Resolver mirror would be nice.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagi
der.com/InChI.asmx/SMILESToInChI?smiles=(O)C
Very fast - xml return:
InChI=1S/C5H12O/c1-3-4-5(2)6/h5-6H,3-4H2,1-2H3
After parsing, you have to keep the InChI= and wrap the whole thing is
%22's for PubChem.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Norm
All-
I kind of lost track of this. It looks like Wikipedia has implemented Jmol
off of SMILES - e.g.
http://en.wikipedia.org/wiki/Chalcone
A one month conversion!
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
. I think all my
problems are javascript calls in IF statements. The } seems to END the IF
if a javascript call is not involved. I have a lot of these javascript
calls, so I'll have to keep my eyes open for ones I might have missed.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinoi
Script('echo @etv2;etv2="";if (fnd == 1){javascript "fbLnk()"}');
}
Here's the console error. It's just related to the last line. From my
testing, the for loop completes and find does find the db item - i.e. etv2
contains the correct information. I don
lgorithm"
This is a conversion, not a look-up.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
--
ng thought: What will Resolver respond to the
actual query "isooctane?" Does Resolver have a sense of industrial chemical
history? How will it respond? I'll let you check!
http://cactus.nci.nih.gov/chemical/structure/isooctane/iupac_name
Otis
--
Otis Rothenberger
Department of Ch
601 - 700 of 1051 matches
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