Thanks Robert. That explains.
_________________________________
Wenhan Chen
School of Chemistry and Molecular Biosciences
The University of Queensland
2013/8/10 Robert Hanson <hans...@stolaf.edu>
> Use the SMILES if you can. The 2D requires MMFF94 minimization, and that
> is what is slowing it down so much.
>
>
> On Thu, Aug 8, 2013 at 10:47 PM, 陈文瀚 <chenwh...@gmail.com> wrote:
>
>> >> Do you have the same trouble at
>> http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm ?
>> It runs really fast. So I downloaded the page and did some simple test
>> locally and it worked quite well.
>> I monitored the network usage, and saw the invoking cactus.nci, but mine
>> didn't do that.
>>
>> Only then I realized instead of passing a SMILES string to the url, by
>> using load SMILES, I used load INLINE to load a string generated by JME
>> with 2D representation of the molecule with atoms and corresponding
>> coordinates like this :
>> 6 6 C 14.93 -4.45 C 14.93 -3.05 C 13.72 -2.35 C 12.51 -3.05 C 12.51
>> -4.45 C 13.72 -5.15 1 2 1 2 3 2 3 4 1 4 5 2 5 6 1 6 1 2
>> Seemed to me the parsing of the string takes ages to finish, then the JME
>> format string returned from cactus.nci. However still I will prefer to
>> parse of the 2D coordinates into 3D. So I am wondering is there a way to
>> make it parse faster?
>>
>> Cheers,
>>
>>
>>
>> _________________________________
>> Wenhan Chen
>> School of Chemistry and Molecular Biosciences
>> The University of Queensland
>>
>>
>>
>> 2013/8/8 Robert Hanson <hans...@stolaf.edu>
>>
>>> Wenhan Chen,
>>>
>>> If you are transferring a SMILES string to Jmol, it will have to go
>>> through the NCI Resolver to get the structure. It's probably that
>>> connection. Do you have jsmol.php set up on your server? Without that, some
>>> browsers won't work at all, because you are doing an AJAX all in JSmol to a
>>> remote server. If you can open a developer console in the browser, check
>>> the network usage and see if it is hanging on a call to NCI.
>>>
>>> Do you have the same trouble at
>>> http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm ?
>>>
>>> Bob
>>>
>>>
>>>
>>> On Wed, Aug 7, 2013 at 11:11 PM, 陈文瀚 <chenwh...@gmail.com> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I am trying to shift my old Jmol routines to Jsmol as a way to avoid
>>>> the disturbing warnings using Applet.
>>>>
>>>> I have long smiles string generated from JME for a relatively larger
>>>> molecule(60 atoms) for unknown reasons it takes ages to get it loaded into
>>>> Jsmol. And the browser kept poping up the warning of script not responsive.
>>>> I am wondering if anyone else experience this before and how to solve it?
>>>>
>>>> Cheers,
>>>>
>>>>
>>>> _________________________________
>>>> Wenhan Chen
>>>> School of Chemistry and Molecular Biosciences
>>>> The University of Queensland
>>>>
>>>>
>>>>
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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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>>> Get 100% visibility into Java/.NET code with AppDynamics Lite!
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>>> Get down to code-level detail for bottlenecks, with <2% overhead.
>>> Download for free and get started troubleshooting in minutes.
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>>>
>>
>>
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>> Download for free and get started troubleshooting in minutes.
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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
>
>
>
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite!
> It's a free troubleshooting tool designed for production.
> Get down to code-level detail for bottlenecks, with <2% overhead.
> Download for free and get started troubleshooting in minutes.
> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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