Re: [Jmol-users] help - Question about JSmol

[Robert Hanson]

What happens when you

1) just download http://chemapps.stolaf.edu/jmol//jsmol.zip, unzip it, and
run jsmol.htm there on your machine. It works, right? With a menu?
2) now upload that directory to a website and try it there. Works or not? I
would think so.
3) now adapt jsmol.htm to your needs or substitute your page and see if
that works.

I think the "standard" development procedure is basically that -- and, if
desired, then removing directories and/or files that are unnecessary. (You
can find out what is required that is not in the "core" directory by
inspecting the info panel "behind" the viewer. using browser developer
tools -- javascript console -- jmolApplet0._showInfo(true)





On Fri, Jan 25, 2013 at 9:00 PM, Jonathan Gough
wrote:

> At the moment, I am using the St. Olaf packages to trouble shoot the
> issues.  If I can't load a simple page that utilizes your code - then in my
> mind there is an issue with the server I am using to host the single page,
> yes?
>
> I have edited the test page again, simplified the header (I think) and
> removed the full path to j2s.  Now it's broken again.  I know it's not the
> header, as when I changed that, it still functioned the same.  therefore
> there is some issue with the j2s statement.
>
> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm
>
>
> On Fri, Jan 25, 2013 at 10:28 AM, Jonathan Gough <
> jonathan.d.go...@gmail.com> wrote:
>
>> Bob,
>>
>> I'm still having a hard time figuring this out.
>>
>> 1 - I believe that the following page is picking up everything from you
>> page, and the right click menu isn't working.  Would the problem be with
>> out server or am I still missing something?
>> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm
>>
>> 2- RE: corrupted files.  What I did previously was, download (via chrome)
>> unzip (via my mac's default application) the jsmol folder was moved to the
>> website directory (in a dropbox folder elsewhere on my mac) and then
>> uploaded to the server via the ftp protocol built into dreamweaver 5.5.
>> That failed so I tried this - used wget to download the file on a linux
>> box (centOS 5).  used bash unzip, scp to the website directory on my mac,
>> then ftp via dreamweaver.  That also failed (and is what is up now).
>>
>> In theory I could ftp straight from the linux box, but I can't figure out
>> exactly how to do that.  Can you advise on how I might proceed?
>>
>> Thanks,
>> Jonathan
>>
>>
>>
>> On Wed, Jan 23, 2013 at 5:09 PM, Jonathan Gough <
>> jonathan.d.go...@gmail.com> wrote:
>>
>>> Thanks for getting back to me Bob,
>>>
>>> I am using a mac, but I didn't edit those files.   In fact, I
>>> re-downloaded everything and the problem is the same.  I even used wget
>>> from a linux box to grab the files from your machine and they are
>>> identical.  if you go to
>>> http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
>>> source, there isn't any gaps.  I used vi, and couldn't see any gaps either.
>>>
>>> if for some reason they are there, how would I go about getting rid of
>>> them?  any other ideas?
>>>
>>> thanks,
>>> Jonathan
>>>
>>>
>>> On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough <
>>> jonathan.d.go...@gmail.com> wrote:
>>>
 Firstly I would like to thank everyone for their hard work on JSmol and
 Jmol; Incredible, I love it!

 I am working on a website to help students here at LIU who are taking
 organic chemistry.

 I believe I have figured out how to implement JSmol.  In my testing
 however, I have only been able to get JSmol.min.js to work.
 For whatever reason, the other, or full packages (JSmoljQuery.js,
 JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
 j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
 doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
 page works, but test2.htm does not.

 the test pages on my site are here

 this works:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm

 this doesn't:
 http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm

 simple-example that works:
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm

 simple-example that doesn't work (missing the JSmol.min.js):
 http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm


 I was wondering if anyone could provide some insight.

 Sincerely,
 Jonathan

>>>
>>>
>>
>
>
> --
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
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Re: [Jmol-users] help - Question about JSmol

[Angel Herráez]

> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm

I am not sure, but it is possible that this line within Info in your page

j2sPath: "j2s",

is read as "find the files in subfolder j2s of the current (i.e. this page) 
folder"
So it's no surprise that it does not load


I think you sopuld put the whole set of JSmol files in your server. Loading 
page and code from a mixture of servers is harder to predict.
I can say that when I first tried to use JSmol and pointed to StOlaf server for 
all the javascript, I could not make it work.



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Re: [Jmol-users] help - Question about JSmol

[Jaime Prilusky]

On Jan 25, 2013, at 9:00 PM, Jonathan Gough wrote:

At the moment, I am using the St. Olaf packages to trouble shoot the issues.  
If I can't load a simple page that utilizes your code - then in my mind there 
is an issue with the server I am using to host the single page, yes?

'loadScript' is unable to find the directory 'core' required for the file 
'package.js'
Declaring the path leading to the required directories is needed.

Jaim
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Re: [Jmol-users] help - Question about JSmol

[Jonathan Gough]

At the moment, I am using the St. Olaf packages to trouble shoot the
issues.  If I can't load a simple page that utilizes your code - then in my
mind there is an issue with the server I am using to host the single page,
yes?

I have edited the test page again, simplified the header (I think) and
removed the full path to j2s.  Now it's broken again.  I know it's not the
header, as when I changed that, it still functioned the same.  therefore
there is some issue with the j2s statement.

http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm


On Fri, Jan 25, 2013 at 10:28 AM, Jonathan Gough  wrote:

> Bob,
>
> I'm still having a hard time figuring this out.
>
> 1 - I believe that the following page is picking up everything from you
> page, and the right click menu isn't working.  Would the problem be with
> out server or am I still missing something?
> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm
>
> 2- RE: corrupted files.  What I did previously was, download (via chrome)
> unzip (via my mac's default application) the jsmol folder was moved to the
> website directory (in a dropbox folder elsewhere on my mac) and then
> uploaded to the server via the ftp protocol built into dreamweaver 5.5.
> That failed so I tried this - used wget to download the file on a linux
> box (centOS 5).  used bash unzip, scp to the website directory on my mac,
> then ftp via dreamweaver.  That also failed (and is what is up now).
>
> In theory I could ftp straight from the linux box, but I can't figure out
> exactly how to do that.  Can you advise on how I might proceed?
>
> Thanks,
> Jonathan
>
>
>
> On Wed, Jan 23, 2013 at 5:09 PM, Jonathan Gough <
> jonathan.d.go...@gmail.com> wrote:
>
>> Thanks for getting back to me Bob,
>>
>> I am using a mac, but I didn't edit those files.   In fact, I
>> re-downloaded everything and the problem is the same.  I even used wget
>> from a linux box to grab the files from your machine and they are
>> identical.  if you go to
>> http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
>> source, there isn't any gaps.  I used vi, and couldn't see any gaps either.
>>
>> if for some reason they are there, how would I go about getting rid of
>> them?  any other ideas?
>>
>> thanks,
>> Jonathan
>>
>>
>> On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough <
>> jonathan.d.go...@gmail.com> wrote:
>>
>>> Firstly I would like to thank everyone for their hard work on JSmol and
>>> Jmol; Incredible, I love it!
>>>
>>> I am working on a website to help students here at LIU who are taking
>>> organic chemistry.
>>>
>>> I believe I have figured out how to implement JSmol.  In my testing
>>> however, I have only been able to get JSmol.min.js to work.
>>> For whatever reason, the other, or full packages (JSmoljQuery.js,
>>> JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
>>> j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
>>> doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
>>> page works, but test2.htm does not.
>>>
>>> the test pages on my site are here
>>>
>>> this works:
>>> http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm
>>>
>>> this doesn't:
>>> http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm
>>>
>>> simple-example that works:
>>> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm
>>>
>>> simple-example that doesn't work (missing the JSmol.min.js):
>>> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm
>>>
>>>
>>> I was wondering if anyone could provide some insight.
>>>
>>> Sincerely,
>>> Jonathan
>>>
>>
>>
>
--
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Re: [Jmol-users] help - Question about JSmol

[Robert Hanson]

On Fri, Jan 25, 2013 at 5:28 PM, Jonathan Gough
wrote:

> Bob,
>
> I'm still having a hard time figuring this out.
>
>
sounds very frustrating. I am 100% sure it is a tool you are using
somewhere along the line, but not being very adept with Macs, I can't
really give you much of a hand. Perhaps a user more familiar with Macs can
suggest a binary file reader -- something that opens files on a Mac and
allows you to look at the binary code. You are looking for 0D 0D 0A.
Whatever program is creating that, that's your problem. You could also go
by file size. The corrupted files are much longer than the correct ones.



> 1 - I believe that the following page is picking up everything from you
> page, and the right click menu isn't working.  Would the problem be with
> out server or am I still missing something?
> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm
>
>
OK, here is what is unusual:

j2sPath: "http://chemapps.stolaf.edu/jmol/jsmol/j2s";


So your idea is to load all the JavaScript from St. Olaf. It certainly
MIGHT work. By the way, you can replace all those .js sources by


http://chemapps.stolaf.edu/jmol/jsmol/
http://chemapps.stolaf.edu/jmol/jsmol/JSmoljQuery.js>JSmol.min.js>

But, the general problem here is that you probably should not link to
chemapps.stolaf.edu that way. I change those files routinely, and my
uploads will likely break your pages while they are happening.

Still, I don't see why exactly it happens only when the menu is loaded.
Very odd!

Bob



> 2- RE: corrupted files.  What I did previously was, download (via chrome)
> unzip (via my mac's default application) the jsmol folder was moved to the
> website directory (in a dropbox folder elsewhere on my mac) and then
> uploaded to the server via the ftp protocol built into dreamweaver 5.5.
> That failed so I tried this - used wget to download the file on a linux
> box (centOS 5).  used bash unzip, scp to the website directory on my mac,
> then ftp via dreamweaver.  That also failed (and is what is up now).
>
> In theory I could ftp straight from the linux box, but I can't figure out
> exactly how to do that.  Can you advise on how I might proceed?
>
> Thanks,
> Jonathan
>
>
>
> On Wed, Jan 23, 2013 at 5:09 PM, Jonathan Gough <
> jonathan.d.go...@gmail.com> wrote:
>
>> Thanks for getting back to me Bob,
>>
>> I am using a mac, but I didn't edit those files.   In fact, I
>> re-downloaded everything and the problem is the same.  I even used wget
>> from a linux box to grab the files from your machine and they are
>> identical.  if you go to
>> http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
>> source, there isn't any gaps.  I used vi, and couldn't see any gaps either.
>>
>> if for some reason they are there, how would I go about getting rid of
>> them?  any other ideas?
>>
>> thanks,
>> Jonathan
>>
>>
>> On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough <
>> jonathan.d.go...@gmail.com> wrote:
>>
>>> Firstly I would like to thank everyone for their hard work on JSmol and
>>> Jmol; Incredible, I love it!
>>>
>>> I am working on a website to help students here at LIU who are taking
>>> organic chemistry.
>>>
>>> I believe I have figured out how to implement JSmol.  In my testing
>>> however, I have only been able to get JSmol.min.js to work.
>>> For whatever reason, the other, or full packages (JSmoljQuery.js,
>>> JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
>>> j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
>>> doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
>>> page works, but test2.htm does not.
>>>
>>> the test pages on my site are here
>>>
>>> this works:
>>> http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm
>>>
>>> this doesn't:
>>> http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm
>>>
>>> simple-example that works:
>>> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm
>>>
>>> simple-example that doesn't work (missing the JSmol.min.js):
>>> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm
>>>
>>>
>>> I was wondering if anyone could provide some insight.
>>>
>>> Sincerely,
>>> Jonathan
>>>
>>
>>
>
>
> --
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
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> Jmol-users@lists.sourceforge.net
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>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.

Re: [Jmol-users] help - Question about JSmol

[Angel Herráez]

Hi Jonathan

I don't think that download or ftp will be your problem. It is a 
zipfile, so the contents will not be altered during file retrieval.
Make sure you are downloading the correct file,
http://chemapps.stolaf.edu/jmol/jsmol.zip

Then it might be a question of how it is unzipped, but I would not 
expect so. As long as you don't edit the files contained in the zip, 
they should be preserved as they were.

(I run Windows, so I cannot really assess exactly the different 
behaviour of CR vs CRLF in the files.)
I have been using the downloaded jsmol.zip without trouble.



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Re: [Jmol-users] help - Question about JSmol

[Jonathan Gough]

Bob,

I'm still having a hard time figuring this out.

1 - I believe that the following page is picking up everything from you
page, and the right click menu isn't working.  Would the problem be with
out server or am I still missing something?
http://myweb.brooklyn.liu.edu/jgough/ChemResources/example3.htm

2- RE: corrupted files.  What I did previously was, download (via chrome)
unzip (via my mac's default application) the jsmol folder was moved to the
website directory (in a dropbox folder elsewhere on my mac) and then
uploaded to the server via the ftp protocol built into dreamweaver 5.5.
That failed so I tried this - used wget to download the file on a linux box
(centOS 5).  used bash unzip, scp to the website directory on my mac, then
ftp via dreamweaver.  That also failed (and is what is up now).

In theory I could ftp straight from the linux box, but I can't figure out
exactly how to do that.  Can you advise on how I might proceed?

Thanks,
Jonathan



On Wed, Jan 23, 2013 at 5:09 PM, Jonathan Gough
wrote:

> Thanks for getting back to me Bob,
>
> I am using a mac, but I didn't edit those files.   In fact, I
> re-downloaded everything and the problem is the same.  I even used wget
> from a linux box to grab the files from your machine and they are
> identical.  if you go to
> http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
> source, there isn't any gaps.  I used vi, and couldn't see any gaps either.
>
> if for some reason they are there, how would I go about getting rid of
> them?  any other ideas?
>
> thanks,
> Jonathan
>
>
> On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough <
> jonathan.d.go...@gmail.com> wrote:
>
>> Firstly I would like to thank everyone for their hard work on JSmol and
>> Jmol; Incredible, I love it!
>>
>> I am working on a website to help students here at LIU who are taking
>> organic chemistry.
>>
>> I believe I have figured out how to implement JSmol.  In my testing
>> however, I have only been able to get JSmol.min.js to work.
>> For whatever reason, the other, or full packages (JSmoljQuery.js,
>> JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
>> j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
>> doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
>> page works, but test2.htm does not.
>>
>> the test pages on my site are here
>>
>> this works:
>> http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm
>>
>> this doesn't:
>> http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm
>>
>> simple-example that works:
>> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm
>>
>> simple-example that doesn't work (missing the JSmol.min.js):
>> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm
>>
>>
>> I was wondering if anyone could provide some insight.
>>
>> Sincerely,
>> Jonathan
>>
>
>
--
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MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
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Re: [Jmol-users] help - Question about JSmol

[Robert Hanson]

On Wed, Jan 23, 2013 at 4:09 PM, Jonathan Gough
wrote:

> Thanks for getting back to me Bob,
>
> I am using a mac, but I didn't edit those files.   In fact, I
> re-downloaded everything and the problem is the same.  I even used wget
> from a linux box to grab the files from your machine and they are
> identical.  if you go to
> http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
> source, there isn't any gaps.  I used vi, and couldn't see any gaps either.
>


That's because those editors were programmed to ignore this sort of
cross-platform problem. Use a binary file reader. You will see. They are
there. Something you did mangled the files. Mine have

%0D%0A

(CR LF)

yours have

%0D%0D%0A

(CR CR LF)

What I did was to view source at the link you sent me, and then I
right-clicked the link to JSmolCore.js and saved that, then looked at it
with a binary file reader I have.

Mine:

008457:   _jsmolfo
008465:   rmdiv__"
008473: <20>   style="
008481:   display:
008489:   none">\  <0D>
008497: <0A> <09> <09> <09> <09>      id="

Yours:

008643:   _jsmolfo
008651:   rmdiv__"
008659: <20>   style="
008667:   display:
008675:   none">\  <0D>
008683: <0D> <0A> <09> <09> <09> <09>      id="

But even just with my browser at your link, above, I see the "double
spacing" line breaks.



Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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Re: [Jmol-users] help - Question about JSmol

[Jonathan Gough]

Thanks for getting back to me Bob,

I am using a mac, but I didn't edit those files.   In fact, I re-downloaded
everything and the problem is the same.  I even used wget from a linux box
to grab the files from your machine and they are identical.  if you go to
http://myweb.brooklyn.liu.edu/jgough/jsmol/JSmolCore.js  and view page
source, there isn't any gaps.  I used vi, and couldn't see any gaps either.

if for some reason they are there, how would I go about getting rid of
them?  any other ideas?

thanks,
Jonathan


On Wed, Jan 23, 2013 at 1:02 PM, Jonathan Gough
wrote:

> Firstly I would like to thank everyone for their hard work on JSmol and
> Jmol; Incredible, I love it!
>
> I am working on a website to help students here at LIU who are taking
> organic chemistry.
>
> I believe I have figured out how to implement JSmol.  In my testing
> however, I have only been able to get JSmol.min.js to work.
> For whatever reason, the other, or full packages (JSmoljQuery.js,
> JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
> j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
> doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
> page works, but test2.htm does not.
>
> the test pages on my site are here
>
> this works:
> http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm
>
> this doesn't:
> http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm
>
> simple-example that works:
> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm
>
> simple-example that doesn't work (missing the JSmol.min.js):
> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm
>
>
> I was wondering if anyone could provide some insight.
>
> Sincerely,
> Jonathan
>
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Re: [Jmol-users] help - Question about JSmol

[Robert Hanson]

Thank you -- glad you find it useful.

When you copied the files, whatever program you used inadvertently added
extra linefeeds between the lines. So You got:

 '\

\

\



instead of

 '\
\
\



and that failed. My guess is that you edited that with some tool that
wasn't properly recognizing the two-character "CR-LF" sequence as a new
line. Perhaps on a Mac? Would TextEdit do that? So it turned those into
"CR-CR-LF" for some reason, and that broke the code.

Bob Hanson





On Wed, Jan 23, 2013 at 12:02 PM, Jonathan Gough  wrote:

> Firstly I would like to thank everyone for their hard work on JSmol and
> Jmol; Incredible, I love it!
>
> I am working on a website to help students here at LIU who are taking
> organic chemistry.
>
> I believe I have figured out how to implement JSmol.  In my testing
> however, I have only been able to get JSmol.min.js to work.
> For whatever reason, the other, or full packages (JSmoljQuery.js,
> JSmolCore.js, JSmolApplet.js, JSmolApi.js, JSmolThree.js, JSmolGLmol.js,
> j2s/j2sjmol.js, JSmol.js) do not want to work; pointing at your site
> doesn't help, neither does switching browsers.  In my hands the Jsmol.htm
> page works, but test2.htm does not.
>
> the test pages on my site are here
>
> this works:
> http://myweb.brooklyn.liu.edu/jgough/jsmol/jsmol.htm
>
> this doesn't:
> http://myweb.brooklyn.liu.edu/jgough/jsmol/test2.htm
>
> simple-example that works:
> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example1.htm
>
> simple-example that doesn't work (missing the JSmol.min.js):
> http://myweb.brooklyn.liu.edu/jgough/ChemResources/example2.htm
>
>
> I was wondering if anyone could provide some insight.
>
> Sincerely,
> Jonathan
>
>
> --
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
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>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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