I observe the same for item 4, with the following error:
Warning: global function “jsmeOnLoad” is not defined. If you have defined it,
there might be a syntax error in your javascript code.
On Nov 4, 2013, at 2:15 PM, Otis Rothenberger <osrot...@chemagic.com> wrote:
>
> 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
>>
>>
>> ------------------------------------------------------------------------------
>> Android is increasing in popularity, but the open development platform that
>> developers love is also attractive to malware creators. Download this white
>> paper to learn more about secure code signing practices that can help keep
>> Android apps secure.
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>> developers love is also attractive to malware creators. Download this white
>> paper to learn more about secure code signing practices that can help keep
>> Android apps secure.
>> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
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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
>>
>> ------------------------------------------------------------------------------
>> Android is increasing in popularity, but the open development platform that
>> developers love is also attractive to malware creators. Download this white
>> paper to learn more about secure code signing practices that can help keep
>> Android apps secure.
>> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk_______________________________________________
>> Jmol-users mailing list
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>
> ------------------------------------------------------------------------------
> Android is increasing in popularity, but the open development platform that
> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk_______________________________________________
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
------------------------------------------------------------------------------
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paper to learn more about secure code signing practices that can help keep
Android apps secure.
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