I don't know if this is related to this thread, but several points:
1) I just noticed that 13.3.9 appears to be broken on an NCI load. Double bonds
are missing on a name load and a SMILES load.
2) The above sdf's are OK, so I think is JSmol
3) PubChem loads are erratically funky. I got several glucose models loaded by
one glucose query. This could be PubChem. I'll check it out/
4) http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm appears broken on Safari
and Chrome.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 4, 2013, at 12:19 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> Jmol's minimization from SMILES is actually very very good -- it does not do
> this itself; instead, it sends it to CACTVS. If there is any delay, it is in
> that call.
>
> It's essential that you use
>
> autoez
>
> as one of the options to JME. JSmol adds that automaticallly. Please try a
> few of your molecules at
>
> http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
>
> and tell me if there are any errors at all, and if so, send me enough
> information that I can reproduce the problem, if you can.
>
> I did see a problem there with 2D -> 3D not being converted properly when
> there is a "\" symbol in the SMILES string. That is fixed now on my site;
> files are at
>
> http://chemapps.stolaf.edu/jmol/jmol-13.3.9_2013.11.04.zip
>
>
>
> Bob
>
>
>
> On Sun, Nov 3, 2013 at 11:43 PM, 陈文瀚 <chenwh...@gmail.com> wrote:
> load SMILES "xxxxxxx" is what I am using. However what I found it, the smiles
> string is not sufficient to depict the original 2D structure.
> Some of the molecules we tried to build lost the double bonds when we get the
> result from the cactus. That's why I am search for alternative
> solutions. So I am thinking of using the 2D representation of the structures
> e.g. the sdf file, but I was not able to foresee the conversion of the sdf
> file to other formats could be so troublesome. I thought it is
> straightforward in babel. However now I am stuck at the adding correct number
> of H atoms
> to the charged atoms in sdf file which is kind of disturbing. Anyway, I still
> am looking for ways to correct the number of H atoms.
>
> cheers,
>
> _________________________________
> Wenhan Chen
> School of Chemistry and Molecular Biosciences
> The University of Queensland
>
>
>
> 2013/11/1 Robert Hanson <hans...@stolaf.edu>
> The CACTVS server at NIH does a great job of turning 2D files into 3D. It's
> best not to have Jmol do that. You can pass the SMILES string from JME to
> Jmol; it will send it off to NIH.
>
> load SMILES "xxxxxxx"
>
>
>
>
> On Tue, Oct 29, 2013 at 7:55 PM, 陈文瀚 <chenwh...@gmail.com> wrote:
> Actually if I transfer the structure from a mol file to JSmol and then try to
> optimize the structure, the charity cannot be preserved as well ...
>
>
>
> _________________________________
> Wenhan Chen
> School of Chemistry and Molecular Biosciences
> The University of Queensland
>
>
>
> 2013/10/30 陈文瀚 <chenwh...@gmail.com>
> Basically, molecules with more than 30 atoms sent in JME format(not including
> H) will cause a halt for the browser as the js try to hold the browser.
> But you are right, it was quick using Jmol with JRE. I think JSmol try to do
> EM using MMFF which takes the most time.
> When the molecule in MOL format passes onto JSmol, it works fine with no EM.
>
> Even so I still am trying to address the problem using mol format, as the
> charge information (the number of H atoms) in the mol file is not presented
> right in JSmol.
>
> Herein is an example :
>
> C+
> / \
> C -- -C
> The mol file for the above mol is :
>
> CWRITER31030r]09392D
> Created with ChemWriter - http://chemwriter.com
> 3 3 0 0 0 0 0 0 0 0999 V2000
>
> 4.3530 -4.7830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.3530 -4.7830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.8530 -3.9169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0
> 2 3 1 0 0 0
> 3 1 1 0 0 0
> M CHG 1 3 1
> M END
>
> JSmol cannot add an H atom to the C+ atom.
>
>
>
>
> _________________________________
> Wenhan Chen
> School of Chemistry and Molecular Biosciences
> The University of Queensland
>
>
>
> 2013/10/30 Angel Herráez <angel.herr...@uah.es>
> Thanks for the feedback, Pino
>
> Then maybe the 3D minimization is much slower in the Javascript
> version that in the Java version.
>
> I've now added an option to the JSME page to check if it is the
> transfer (unlikely), adding the hydrogens or the 3D minimization
> which gives the delay
> That is only useful for MOL transfer.
> JME transfer must necessarily go to 3D conversion, that may be the
> bottleneck.
>
> It seems indeed that it is the JmeReader routine that takes its time
>
>
>
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> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
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> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
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