/wedged bonds where they are not needed.
Mike
*From:* Robert Hanson [mailto:hans...@stolaf.edu]
*Sent:* 22 January 2014 03:10
*To:* jmol-users@lists.sourceforge.net
*Subject:* Re: [Jmol-users] Jmol 14.0.6 released
The nice thing about Jmol's SMILES comparisons is that it is totally
[mailto:hans...@stolaf.edu]
Sent: 22 January 2014 03:10
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.0.6 released
The nice thing about Jmol's SMILES comparisons is that it is totally
independent of what program was used to make the SMILES string in the first
place
On Tue, Jan 21, 2014 at 1:15 AM, Otis Rothenberger osrot...@chemagic.comwrote:
Bob,
The following Jmol script runs cross domain:
var x = load(http://chemagic.com/models.aspx?smi2stdinchi=CCC;);var y =
load(http://chemagic.com/models.aspx?inchi2cas=; + x);var z =
Bob and Pino
Possibly. At least for known compounds. Does this fail gracefully?
NIST fails gracefully because they return a data not found graphic image. I've
never encountered a NIST server down issue, so I'm not sure what happens there.
The biggest problem with SMILES to InChI is
that switching sounds good for real (known) structures.
Q: How are you accessing chem spider? Is the idea there that you have a
registration key used only by your server?
On Tue, Jan 21, 2014 at 10:38 AM, Otis Rothenberger
osrot...@chemagic.comwrote:
Bob and Pino
Possibly. At least for
Bob,
This is for basic Web textbook stuff, so real structures are not a problem.
I'm just using the ChemSpider InChI service:
http://www.chemspider.com/InChI.asmx
For SMILES to InChI by GET they have not required a security token up to this
point in time. SMILES to InChI and InChIKey is the
On Tue, Jan 21, 2014 at 12:46 PM, Otis Rothenberger
osrot...@chemagic.comwrote:
Bob,
This is for basic Web textbook stuff, so real structures are not a problem.
I'm just using the ChemSpider InChI service:
http://www.chemspider.com/InChI.asmx
For SMILES to InChI by GET they have not
Bob:
As I recall, several years ago you wrote the java applet to compare -smiles
strings. The issue for me before that came along was that drawing a structure
in JME could result in more than one “correct” smiles string, depending on how
it was drawn, particularly in regards to
Bob and Phil,
Two responses here.
Bob, Because I completely forgot about that option! Now that we have both JMSE
and Jmol on each text page, that's the logical thing to do.
Phil, Unique SMILES in JSME is an option that must be set. BUT, and it's a
big BUT, this does not work for stereo SMILES
Afterthought:
Phil, that's the neat thing about what Bob suggested. It takes unique SMILES
off the table.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jan 21, 2014, at 3:23 PM, Otis Rothenberger osrot...@chemagic.com wrote:
Bob and Phil,
Two responses here.
The nice thing about Jmol's SMILES comparisons is that it is totally
independent of what program was used to make the SMILES string in the first
place. There is no need for a canonical string for our purposes (as there
might be for database look-ups). Thus, it matches any matching structure,
Apologies. I have had to unrelease 14.0.6.
Only significant if you use the model parameter on echos or isosurfaces.
I will get another version out later today.
On Sun, Jan 19, 2014 at 6:08 PM, Robert Hanson hans...@stolaf.edu wrote:
see
Sure, that would be fine. It is what I am working on right now, actually.
But this is 1H NMR. Still working on 13C prediction. No similar page for
IR.
On Mon, Jan 20, 2014 at 2:47 PM, pino.stricc...@libero.it
pino.stricc...@libero.it wrote:
Bob, I want to add to my blog the page (
Bob,
The following Jmol script runs cross domain:
var x = load(http://chemagic.com/models.aspx?smi2stdinchi=CCC;);var y =
load(http://chemagic.com/models.aspx?inchi2cas=; + x);var z =
http://webbook.nist.gov/cgi/cbook.cgi?Spec=C; + y +
Index=0Type=IRLarge=onSVG=on;show url @z
First a
see https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0
This version has a variety of bug fixes:
___JmolVersion=14.1.6
bug fix: Jmol2.js should have commented lines in Jmol.Info but does not
bug fix: translucent geosurface was disabled;
bug fix: select visible not right after this
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