Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

[Rolf Huehne]

On 12/16/2015 09:48 PM, Robert Hanson wrote:
> Jmol uses typed arrays when possible. Parsing of scripts is relatively
> slow. Rolf, if you want to give me something to try, I will be happy to
> play with it and see what I can learn.
>
Bob, what would you want to have?

I think I cannot reveal the whole system yet, but I have placed here 
(temporarily) the compressed output of 'write var ...' of the parsed data.

Uncompressed it is about 73 megabytes and JSmol/Java needs at least 500 
megabyte RAM to handle it.

Regards,
Rolf
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Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
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Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
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Re: [Jmol-users] "labels off" freezing JSmol

[Rolf Huehne]

On 12/17/2015 04:39 AM, Robert Hanson wrote:
> Wow, what a GREAT FIND, Eric! Say you have a set of information in the form
> of an array for n items. Now you need to set the value for n+1. Well, of
> course you were efficient in your creating an array of just n values, so
> now you have to create a NEW array that is n+1 long instead of n long.
> That's pretty fast, if you do it once. But now do this:
>
> a = [];
> for (i = 0; i < 2; i++) {
>if (a.length < i + 1)
>  a = copyArray(a, i + 1);
> }
>
> See the problem? Not only are you creating an array that is 2 long, you
> are creating a new array from an old one *2 times. *Ouch!
>
Bob, I also tried to avoid this in Jmol scripting by setting the last 
value of an array first:

   var parsedData = [];
   parsedData[tsvData.size] = 0;

Would you confirm that this will actually work?

Regards,
Rolf


-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@leibniz-fli.de
Website: http://www.leibniz-fli.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

VAT No: DE 153 925 464
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Tax Number: 162/141/08228


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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

[Rolf Huehne]

On 12/17/2015 04:03 PM, Rolf Huehne wrote:
>> I think I cannot reveal the whole system yet, but I have placed here
>> (temporarily) the compressed output of 'write var ...' of the parsed data.
>>
> Sorry, I forgot the URL:
>
> http://jenalib.fli-leibniz.de/ImgLibPDB/tmp/parsed_data-2015_12_17.zip
>
I have added now also the 'write var ...' output of a smaller subset and 
the loaded TSV files to the ZIP file.

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@leibniz-fli.de
Website: http://www.leibniz-fli.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

VAT No: DE 153 925 464
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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

[Kubasik, Matthew A.]

Bob,

Could you expand on your comment that “Jmol uses typed arrays when possible"?

I am in the habit of initializing arrays with a line like:

a=array()

Should I be doing something else?  Does the array get “typed” after I add an 
entry?

Matt

On Dec 16, 2015, at 3:48 PM, Robert Hanson 
> wrote:

Jmol uses typed arrays when possible. Parsing of scripts is relatively slow. 
Rolf, if you want to give me something to try, I will be happy to play with it 
and see what I can learn.

On Wed, Dec 16, 2015 at 12:30 PM, Paul PILLOT 
> wrote:
Hi Rolf,
my experience in this area is not JSmol related, but when I had to deal with 
big tables in javascript (for a multiple sequence alignment script, aligning 2 
sequences of 5000 signs, requires at least 1 table of 5000 rows and 5000 
columns), I noticed that :
- using integers only tables is fastest
- opting for one dimensional array instead of two dimensional didn’t make a 
noticeable difference
- using typed arrays in some cases improved significantly the performance ( see 
https://developer.mozilla.org/en/docs/Web/JavaScript/Typed_arrays ). This was 2 
years ago, and the browsers’ engine landscape can be quickly moving...
When you parse your data from your TSV file, are the fields stored as text ?

My 2 cents,
Paul

Le 16-12-2015 à 13:12, Rolf Huehne 
> a écrit :

Hi all,

I am looking for some speedup tips for Jmol scripting in JSmol/HTML5.

The speed difference between JSmol/Java and JSmol/HTML5 for graphical
operations like rotation and zooming seems to be about 10 times or less
in Firefox and Chrome (if you don't consider the recent rotation speed
problems in Chrome).

Unfortunately the difference for Jmol scripting seems to be much higher
in my experience: about 50-70 times.

If I load for example 3 TSV (tab separated value) format files with
overall about 34,000 lines, JSmol/Java needs about 26 seconds for
laoding and parsing the data and putting it into a multi-level hash
structure. JSmol/HTML5 needs about 1700 seconds instead.

I already tried to write the final data structure into a file with
'write VAR ...' and read it in again as a script (after adding a proper
variable assignment) but this already took in Java endlessly (I stopped
waiting after more than an hour...).

Q: Does anyone have any other ideas that might speed up this process?

Regards,
Rolf


--

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@leibniz-fli.de
Website: http://www.leibniz-fli.de

  Scientific Director: Prof. Dr. K. Lenhard Rudolph
   Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

VAT No: DE 153 925 464
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Chair, Department 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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Re: [Jmol-users] "labels off" freezing JSmol

[Rolf Huehne]

On 12/17/2015 04:18 PM, Robert Hanson wrote:
> On Thu, Dec 17, 2015 at 8:30 AM, Rolf Huehne  wrote:
>
>> On 12/17/2015 04:39 AM, Robert Hanson wrote:
>>> Wow, what a GREAT FIND, Eric! Say you have a set of information in the
>> form
>>> of an array for n items. Now you need to set the value for n+1. Well, of
>>> course you were efficient in your creating an array of just n values, so
>>> now you have to create a NEW array that is n+1 long instead of n long.
>>> That's pretty fast, if you do it once. But now do this:
>>>
>>> a = [];
>>> for (i = 0; i < 2; i++) {
>>> if (a.length < i + 1)
>>>   a = copyArray(a, i + 1);
>>> }
>>>
>>> See the problem? Not only are you creating an array that is 2 long,
>> you
>>> are creating a new array from an old one *2 times. *Ouch!
>>>
>> Bob, I also tried to avoid this in Jmol scripting by setting the last
>> value of an array first:
>>
>> var parsedData = [];
>> parsedData[tsvData.size] = 0;
>>
>> Would you confirm that this will actually work?
>>
>>
> When I tried this:
>
> t = now()
> a = []
> a[2] = 0
> for (i = 1; i < 2; i++) a.push(i)
> print now(t)
>
> t = now()
> a = []
> for (i = 1; i < 2; i++) a.push(i)
> print now(t)
>
> I found the first was about 5% faster than the second in both Java and
> HTML5. You could experiment yourself with that.
>
I got mixed results:

In Java the first one was much slower than the second one (210,142) in 
the first run. In subsequent runs the times were more similar (72,71; 
69,75; 69,70; 69,70).

In HTML5 the second one was always slightly faster (3277,3177; 
3248,3136; 3164,3146; 3632,3543; 3565,3419).

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@leibniz-fli.de
Website: http://www.leibniz-fli.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

VAT No: DE 153 925 464
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Re: [Jmol-users] "labels off" freezing JSmol

[Robert Hanson]

On Thu, Dec 17, 2015 at 8:30 AM, Rolf Huehne  wrote:

> On 12/17/2015 04:39 AM, Robert Hanson wrote:
> > Wow, what a GREAT FIND, Eric! Say you have a set of information in the
> form
> > of an array for n items. Now you need to set the value for n+1. Well, of
> > course you were efficient in your creating an array of just n values, so
> > now you have to create a NEW array that is n+1 long instead of n long.
> > That's pretty fast, if you do it once. But now do this:
> >
> > a = [];
> > for (i = 0; i < 2; i++) {
> >if (a.length < i + 1)
> >  a = copyArray(a, i + 1);
> > }
> >
> > See the problem? Not only are you creating an array that is 2 long,
> you
> > are creating a new array from an old one *2 times. *Ouch!
> >
> Bob, I also tried to avoid this in Jmol scripting by setting the last
> value of an array first:
>
>var parsedData = [];
>parsedData[tsvData.size] = 0;
>
> Would you confirm that this will actually work?
>
>
When I tried this:

t = now()
a = []
a[2] = 0
for (i = 1; i < 2; i++) a.push(i)
print now(t)

t = now()
a = []
for (i = 1; i < 2; i++) a.push(i)
print now(t)

I found the first was about 5% faster than the second in both Java and
HTML5. You could experiment yourself with that.

Jmol uses a Java List for its internal variable arrays, and when more room
is needed for those, it is added by increasing the array size by at least
1/2, with the starting size is 10.  So if you did this:

a = []
for (i = 1; i < 2; i++) a.push(i)

the array would be copied about 20 times, I think.

Bob

ps -- Eric, this is fixed, and there is no longer any delay. I'll get you
that as a chemapps zip file.
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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

[Robert Hanson]

On Thu, Dec 17, 2015 at 9:26 AM, Kubasik, Matthew A.  wrote:

> Bob,
>
> Could you expand on your comment that “Jmol uses typed arrays when
> possible"?
>
> I am in the habit of initializing arrays with a line like:
>
> a=array()
>
> Should I be doing something else?  Does the array get “typed” after I add
> an entry?
>
>
You can use that or just

a = []

These user-generated arrays are not typed. Jmol internally uses JavaScript
integer and float arrays when possible.

Bob
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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

[Robert Hanson]

We should probably think about being able to switch back and forth between
Jmol variables and JavaScript variables without using JSON. At least for
the HTML5 version.

On Thu, Dec 17, 2015 at 11:04 AM, Robert Hanson  wrote:

> If I were to be able to read that back into Jmol it would need to be in
> JSON format. You would need to use:
>
> x = format("JSON",parsedData)
> write var x "t.json"
>
> and I am not certain that even then Jmol could read it,  but if it could,
> it would be by using
>
> y = eval(load("t.json"))
>
> Maybe you can experiment some, Rolf, and see what particular parsing
> actions lead to this slow down. Could be something that's fixable.
>
> Bob
> ​
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

[Rolf Huehne]

On 12/17/2015 06:04 PM, Robert Hanson wrote:
> If I were to be able to read that back into Jmol it would need to be in
> JSON format. You would need to use:
>
> x = format("JSON",parsedData)
> write var x "t.json"
>
> and I am not certain that even then Jmol could read it,  but if it could,
> it would be by using
>
> y = eval(load("t.json"))
>
> Maybe you can experiment some, Rolf, and see what particular parsing
> actions lead to this slow down. Could be something that's fixable.
>
Thank you for the hint, Bob.
I have thought about using JSON format but couldn't find a way to read 
it in again in the documentation.
And besides I had a lot of trouble with the JSON format in another 
project (Javascript->JSON->Perl-CGI->Filesystem->Perl-CGI->Javascript). 
So I didn't try to dig deeper into it here.

In Java the import of the small dataset in JSON format does work fine.
The import of the full dataset is still running since several minutes. 
So it is much slower there than building the data structure from the TSV 
files.

In HTML5 in Firefox 42 on Linux I got the following error message when I 
tried to import the small dataset in JSON format:

- Error Message --
TypeError: b.lineNumbers is null try/catch path:
0 function (b,d)
  args[0]=TypeError: b.lineNumbers is null
  args[1]=function (){a.instantialize(this,arguments)}
1 JS.ScriptEval.evaluate(a,b,c)
  args[0]=   http://jenalib.fli-leibniz.de/ImgLibPDB/tmp/parsed_data-2015_12_17.zip).

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@leibniz-fli.de
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   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228


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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

[Robert Hanson]

If I were to be able to read that back into Jmol it would need to be in
JSON format. You would need to use:

x = format("JSON",parsedData)
write var x "t.json"

and I am not certain that even then Jmol could read it,  but if it could,
it would be by using

y = eval(load("t.json"))

Maybe you can experiment some, Rolf, and see what particular parsing
actions lead to this slow down. Could be something that's fixable.

Bob
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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

[Robert Hanson]

On Thu, Dec 17, 2015 at 11:51 AM, Rolf Huehne 
wrote:

>
> - Error Message --
> TypeError: b.lineNumbers is null try/catch path:
> 0 function (b,d)
>   args[0]=TypeError: b.lineNumbers is null
>   args[1]=function (){a.instantialize(this,arguments)}
> 1 JS.ScriptEval.evaluate(a,b,c)
>   args[0]=args[1]=true
>   args[2]=false
>


That looks a lot like a "file not found" message to me.
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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

[Rolf Huehne]

On 12/17/2015 07:28 PM, Robert Hanson wrote:
> On Thu, Dec 17, 2015 at 11:51 AM, Rolf Huehne 
> wrote:
>
>>
>> - Error Message --
>> TypeError: b.lineNumbers is null try/catch path:
>> 0 function (b,d)
>>args[0]=TypeError: b.lineNumbers is null
>>args[1]=function (){a.instantialize(this,arguments)}
>> 1 JS.ScriptEval.evaluate(a,b,c)
>>args[0]= >args[1]=true
>>args[2]=false
>>
>
>
> That looks a lot like a "file not found" message to me.
>
You are right, Bob. I took the wrong Jmol-Viewer-Tab. The viewer is 
there on a web server and not loaded locally as I expected.
after changing the URL JSmol/HTML could load the small JSON file 
correctly (about 10 times slower than Java).
Since the Java version has still not finished loading the full dataset 
after about 90 minutes I don't think it makes sense to try it in the 
HTML5 version.

I also tried the local HTML5 version with the small JSON file but it 
loading the file was refused:

--- Error message -
TypeError: b.lineNumbers is null try/catch path:
0 function (b,d)
  args[0]=TypeError: b.lineNumbers is null
  args[1]=function (){a.instantialize(this,arguments)}
1 JS.ScriptEval.evaluate(a,b,c)
  args[0]=NS_ERROR_DOM_BAD_URI: Access to restricted URI denied
  args[1]=true
  args[2]=false
2 JS.ScriptEval.evaluateExpression(a,b,c)
  args[0]=NS_ERROR_DOM_BAD_URI: Access to restricted URI denied
  args[1]=true
  args[2]=false
3 JV.Viewer.evaluateExpressionAsVariable(a)
  args[0]=NS_ERROR_DOM_BAD_URI: Access to restricted URI denied
4 JS.MathExt.evaluateScript(d,a,b)
  args[0]=[JS.ScriptMathProcessor object]
  args[1]=Token[string(4/0x4) value="NS_ERROR_DOM_BAD_URI: Access to r...
  args[2]=134218253
5 JS.MathExt.evaluate(d,a,b,c)
  args[0]=[JS.ScriptMathProcessor object]
  args[1]=Token[keyword(13/0x800020d) value="eval"]
  args[2]=Token[string(4/0x4) value="NS_ERROR_DOM_BAD_URI: Access to r...
  args[3]=134218253
6 JS.ScriptMathProcessor.evaluateFunction(a)
  args[0]=134218253
7 JS.ScriptMathProcessor.addOpAllowMath(a,b,c)
  args[0]=Token[keyword(17/0x1011) value=")"]
  args[1]=true
  args[2]=0
8 JS.ScriptMathProcessor.addOp(a)
  args[0]=Token[keyword(17/0x1011) value=")"]
9 JS.ScriptExpr.parameterExpression(a,b,c,e,f,d,h,g,s,n)
  args[0]=2
  args[1]=9
  args[2]=[JS.ScriptMathProcessor object]
  args[3]=true
  args[4]=0
  args[5]=-1
  args[6]=1
  args[7]=null
  args[8]=null
  args[9]=false
---

Are there additional restrictions of HTML5 versus Java file loading that 
I forgot about?

Regards,
Rolf

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Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
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Phone:   +49 3641 65 6205
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E-Mail:  rhue...@leibniz-fli.de
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Re: [Jmol-users] Let's try this one: Jmol-14.4.1_2015.12.15

[Robert Hanson]

I note that this fix breaks MSIE 9 (about 334 of 253,000 sessions last
month). Next update will have that fixed.

On Wed, Dec 16, 2015 at 2:08 PM, Eric Martz 
wrote:

> Excellent! JSmol/HTML5 appears to rotate acceptably in Chrome (still
> rotates more smoothly in Firefox), and Java works.
>
> Preliminary tests with FirstGlance have revealed no bugs or issues.
>
> I have replaced the jsmol in FirstGlance.Jmol.Org with the December 15
> jsmol.
>
> Thanks so much Bob!!!
> Eric
>
>
> On 12/15/15 9:02 PM, Robert Hanson wrote:
>
> * Download Jmol-14.4.1_2015.12.15-binary.zip (60.7 MB)
>  *
>
>
> Jmol.___JmolVersion="14.4.1_2015.12.15"
>
> bug fix: Bad build for Jmol Java applet
> bug fix: JSmol (JSmolCore.js) check for MS Edge browser, which does not
> support dataURI (so write xxx.png did not work in MS Edge)
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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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Re: [Jmol-users] JSmol 14.4.1 - Javascript error messages in Firefox 42

[Robert Hanson]

Hooray! And that will not be necessary in the next release

On Thu, Dec 17, 2015 at 6:26 AM, Rolf Huehne  wrote:

> On 12/17/2015 12:27 AM, Robert Hanson wrote:
> > Please do give that a try and report back if the "syntax error" message
> > disappear. I had never made the connection that those were only when
> > loading local files.
> >
> The syntax error messages I reported are all gone  in Firefox on MacOS X
> Mavericks and Linux after I added the setting to my page.
>
> Regards,
> Rolf
>
> --
>
> Rolf Huehne
> Postdoc
>
> Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
> Beutenbergstrasse 11
> 07745 Jena, Germany
>
> Phone:   +49 3641 65 6205
> Fax: +49 3641 65 6210
> E-Mail:  rhue...@leibniz-fli.de
> Website: http://www.leibniz-fli.de
>
>Scientific Director: Prof. Dr. K. Lenhard Rudolph
> Head of Administration: Dr. Daniele Barthel
> Chairman of Board of Trustees: Burkhard Zinner
>
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> Register of Associations: No. 230296, Amtsgericht Jena
> Tax Number: 162/141/08228
>
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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Re: [Jmol-users] JSmol 14.4.1 - Javascript error messages in Firefox 42

[Rolf Huehne]

On 12/17/2015 12:27 AM, Robert Hanson wrote:
> Please do give that a try and report back if the "syntax error" message
> disappear. I had never made the connection that those were only when
> loading local files.
>
The syntax error messages I reported are all gone  in Firefox on MacOS X 
Mavericks and Linux after I added the setting to my page.

Regards,
Rolf

-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@leibniz-fli.de
Website: http://www.leibniz-fli.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228


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[Jmol-users] JSmol speed vs. browsers

[Eric Martz]

I have provided data, methods and detailed conclusions here
*http://proteopedia.org/w/JSmol/Rotation_Speeds*
Briefly I found:

For JSmol (HTML5/javascript) Firefox outperforms Chrome, Opera and Edge 
by about four-fold.


Safari is as fast as Firefox with JSmol.

Internet Explorer 11 is unusably slow with JSmol, about 9-fold slower 
than Firefox.


Java is only 1.4-1.8 fold faster in Firefox, but more than 20-fold 
faster in Internet Explorer.


Curiously, rotating/spinning a spacefilled rendering is twice as fast as 
a cartoon rendering in Chrome and Opera (but not in Firefox, Edge or 
Internet Explorer 11).


Thus, in an update I'm preparing for FirstGlance, when using JSmol, 
Firefox will be recommended, and Internet Explorer will be strongly 
discouraged. This is a change since mid-2014, when Chrome outperformed 
Firefox with JSmol.


When using Java, the browser doesn't matter, except that Chrome and Edge 
don't support Java, and Opera threatens to follow suit.


-Eric
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