Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

2015-12-14 Thread Eric Martz 

I have replaced jsmol in FirstGlance in Jmol with the 12/13 version.
Indeed the Chrome disaster seems fixed. And in a quick check, 
FirstGlance appeared to work correctly.


Hurray for Bob! I am constantly in awe! (And yes Yay for Mighty Mouse to 
the rescue!)


Mouse rotation in Chrome is still jerkier than in Firefox, but it is 
acceptable. (Better than Internet Explorer or Edge.)


zoomto *1.3 # default 1 sec

in a large Jmol (as in FirstGlance) is slower, jerkier, and takes 
several seconds in Chrome, but is smooth and fast in Firefox.


(At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm, how about an option 
to increase the size of JSmol by 2.5 fold?)


My impression is that the jerky rotation in Chrome (jerkiness that 
remains in the 12/13 version of JSmol) has been present well before the 
disastrous version 47 of Chrome released December 1.


I wonder if you can do anything further, Bob, to make rotation-via-mouse 
smoother in Chrome, more like it is in Firefox? Just a thought. You've 
already worked a miracle overnight!


-Eric

On 12/13/15 1:56 PM, Robert Hanson wrote:

This new version is now available at SourceForge:

*Download Jmol-14.4.1_2015.12.13-binary.zip (60.3 MB) 
*



*IMPORTANT*: A very recent modification of Chrome makes Chrome 
unusable with all previous versions of JSmol, at least until sometime 
in January. The WebGL version of JSmol is not impacted.


This appears to be the result of a well-meaning attempt by Chromium 
developers to enhance smooth scrolling of pages by lowering the 
priority of setTimeout calls. However, the unanticipated fallout of 
that change results in extremely rough rotation of models. You can 
follow the issue here: 
https://code.google.com/p/chromium/issues/detail?id=568725 Note that 
one of the last comments on Dec. 11 indicates that there indicates 
this issue will not be addressed until sometime in January.


*But there is a workaround. *This release of Jmol 14.4.1 should 
correct that problem and, at the same time, may improve performance 
with Microsoft Edge.


I have put up two versions of JSmol that illustrate the problem and 
the fix:


(original) http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
(fixed) http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm

Testing of that second site would be appreciated.

The work-around is simple, and if you want, you can implement this 
yourself on your site.  Really (in terms of this bug) it is just a 
single coding change in jsmol/js/JSmol.js, where one "setTimeout(f)" 
has been replaced with "requestAnimationFrame(f)". Thus, if you 
prefer, you should be able to just swap in a new JSmol.min.js or 
JSmol.min.nojq.js for the old one. I have not tried this. Of course, 
if you do that, then the other bugs listed below will still be there. 
If you want to try that, here is the link to that file specifically:


http://chemapps.stolaf.edu/jmol/jsmol2/JSmol.min.js

Bob

Jmol.___JmolVersion="14.4.1_2015.12.13"

bug fix: JavaScript Chrome/Edge fix for slow response due to 
setTimeout issues; uses requestAnimationFrame instead in JSmol.js

bug fix: zoomTo not setting time to 0 in the case of scriptWait
bug fix: set selectAllModels should restrict action of display/hide as 
well

bug fix: set selectAllModels not working appropriately
bug fix: set selectAllModels should not be saved in state
bug fix: JmolData.jar does not update atom screen positions upon 
REFRESH or select {visible}

bug fix: JmolData.jar -p flag does not work properly
bug fix: model 0 issued when more than one PDB file is open does not 
execute model *


--
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 14.4.1_2015.12.13 released - IMPORTANT

2015-12-13 Thread Robert Hanson 
Sorry about the link - I ended up changing that (original, broken) link
from "jsmol2" to http://chemapps.stolaf.edu/jmol/jsmol-2015-12-13/jsmol.htm

Yes, Fausto, that is correct. It was an easy fix, at least for a first try.
We have to see if this sluggishness returns in additional cases, but for
the most part this seems to take care of it.
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Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

2015-12-13 Thread J. Bays 
That dates us Otis😩

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

> On Dec 13, 2015, at 4:04 PM, Otis Rothenberger  wrote:
>
> I’m probably not supposed to do this, but the words of Mighty Mouse seem 
> appropriate to yet another Hanson save:
>
> MIGHTY MOUSE THEME SONG
> (Philip Scheib / Marshall Barer) - circa 1955
>
> "Mr. trouble never hangs around,
> when he hears this Mighty sound,
>
> Here I come to save the day!
> That means that Mighty Mouse is on the way!
>
> Yes sir, when there is a wrong to right,
> Mighty Mouse will join the fight!…”
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
>
> --
> ___
> Jmol-users mailing list
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Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

2015-12-13 Thread Otis Rothenberger 
I’m probably not supposed to do this, but the words of Mighty Mouse seem 
appropriate to yet another Hanson save:

MIGHTY MOUSE THEME SONG
(Philip Scheib / Marshall Barer) - circa 1955

"Mr. trouble never hangs around,
when he hears this Mighty sound,

Here I come to save the day!
That means that Mighty Mouse is on the way!

Yes sir, when there is a wrong to right,
Mighty Mouse will join the fight!…”

Otis

--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com





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Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

2015-12-13 Thread Philip Bays 
I concur with Otis, at least on my local server.

Phil

> On Dec 13, 2015, at 2:42 PM, Otis Rothenberger  wrote:
> 
> Bob,
> 
>  http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm 
>    on Chrome Mac (Latest 
> versions OS and Chrome) works fine after cache clear.
> 
> On my site, I swapped out JSmol.min.nojq.js and this also works fine after 
> cache clear.
> 
> “Fine” means a quick check. I’ll play around a bit to make sure.
> 
> Otis
> 
> --
> Otis Rothenberger
> o...@chemagic.com 
> http://chemagic.com
> 
>> On Dec 13, 2015, at 1:56 PM, Robert Hanson > > wrote:
>> 
>> This new version is now available at SourceForge:
>> 
>> Download Jmol-14.4.1_2015.12.13-binary.zip (60.3 MB) 
>> 
>> 
>> 
>> IMPORTANT: A very recent modification of Chrome makes Chrome unusable with 
>> all previous versions of JSmol, at least until sometime in January. The 
>> WebGL version of JSmol is not impacted. 
>> 
>> This appears to be the result of a well-meaning attempt by Chromium 
>> developers to enhance smooth scrolling of pages by lowering the priority of 
>> setTimeout calls. However, the unanticipated fallout of that change results 
>> in extremely rough rotation of models. You can follow the issue here: 
>> https://code.google.com/p/chromium/issues/detail?id=568725 
>>   Note that one 
>> of the last comments on Dec. 11 indicates that there indicates this issue 
>> will not be addressed until sometime in January. 
>> 
>> But there is a workaround. This release of Jmol 14.4.1 should correct that 
>> problem and, at the same time, may improve performance with Microsoft Edge. 
>> 
>> I have put up two versions of JSmol that illustrate the problem and the fix:
>> 
>> (original) http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm 
>> 
>> (fixed) http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm 
>> 
>> 
>> Testing of that second site would be appreciated.
>> 
>> The work-around is simple, and if you want, you can implement this yourself 
>> on your site.  Really (in terms of this bug) it is just a single coding 
>> change in jsmol/js/JSmol.js, where one "setTimeout(f)" has been replaced 
>> with "requestAnimationFrame(f)". Thus, if you prefer, you should be able to 
>> just swap in a new JSmol.min.js or JSmol.min.nojq.js for the old one. I have 
>> not tried this. Of course, if you do that, then the other bugs listed below 
>> will still be there. If you want to try that, here is the link to that file 
>> specifically:
>> 
>> http://chemapps.stolaf.edu/jmol/jsmol2/JSmol.min.js 
>> 
>> 
>> Bob
>> 
>> Jmol.___JmolVersion="14.4.1_2015.12.13"
>> 
>> bug fix: JavaScript Chrome/Edge fix for slow response due to setTimeout 
>> issues; uses requestAnimationFrame instead in JSmol.js 
>> bug fix: zoomTo not setting time to 0 in the case of scriptWait
>> bug fix: set selectAllModels should restrict action of display/hide as well
>> bug fix: set selectAllModels not working appropriately
>> bug fix: set selectAllModels should not be saved in state
>> bug fix: JmolData.jar does not update atom screen positions upon REFRESH or 
>> select {visible}
>> bug fix: JmolData.jar -p flag does not work properly
>> bug fix: model 0 issued when more than one PDB file is open does not execute 
>> model *
>> 
>> -- 
>> 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
>> 
>> --
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net 
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu


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Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

2015-12-13 Thread Otis Rothenberger 
Bob,

 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm 
   on Chrome Mac (Latest 
versions OS and Chrome) works fine after cache clear.

On my site, I swapped out JSmol.min.nojq.js and this also works fine after 
cache clear.

“Fine” means a quick check. I’ll play around a bit to make sure.

Otis

--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com

> On Dec 13, 2015, at 1:56 PM, Robert Hanson  wrote:
> 
> This new version is now available at SourceForge:
> 
> Download Jmol-14.4.1_2015.12.13-binary.zip (60.3 MB) 
> 
> 
> 
> IMPORTANT: A very recent modification of Chrome makes Chrome unusable with 
> all previous versions of JSmol, at least until sometime in January. The WebGL 
> version of JSmol is not impacted. 
> 
> This appears to be the result of a well-meaning attempt by Chromium 
> developers to enhance smooth scrolling of pages by lowering the priority of 
> setTimeout calls. However, the unanticipated fallout of that change results 
> in extremely rough rotation of models. You can follow the issue here: 
> https://code.google.com/p/chromium/issues/detail?id=568725 
>   Note that one 
> of the last comments on Dec. 11 indicates that there indicates this issue 
> will not be addressed until sometime in January. 
> 
> But there is a workaround. This release of Jmol 14.4.1 should correct that 
> problem and, at the same time, may improve performance with Microsoft Edge. 
> 
> I have put up two versions of JSmol that illustrate the problem and the fix:
> 
> (original) http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm 
> 
> (fixed) http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm 
> 
> 
> Testing of that second site would be appreciated.
> 
> The work-around is simple, and if you want, you can implement this yourself 
> on your site.  Really (in terms of this bug) it is just a single coding 
> change in jsmol/js/JSmol.js, where one "setTimeout(f)" has been replaced with 
> "requestAnimationFrame(f)". Thus, if you prefer, you should be able to just 
> swap in a new JSmol.min.js or JSmol.min.nojq.js for the old one. I have not 
> tried this. Of course, if you do that, then the other bugs listed below will 
> still be there. If you want to try that, here is the link to that file 
> specifically:
> 
> http://chemapps.stolaf.edu/jmol/jsmol2/JSmol.min.js 
> 
> 
> Bob
> 
> Jmol.___JmolVersion="14.4.1_2015.12.13"
> 
> bug fix: JavaScript Chrome/Edge fix for slow response due to setTimeout 
> issues; uses requestAnimationFrame instead in JSmol.js 
> bug fix: zoomTo not setting time to 0 in the case of scriptWait
> bug fix: set selectAllModels should restrict action of display/hide as well
> bug fix: set selectAllModels not working appropriately
> bug fix: set selectAllModels should not be saved in state
> bug fix: JmolData.jar does not update atom screen positions upon REFRESH or 
> select {visible}
> bug fix: JmolData.jar -p flag does not work properly
> bug fix: model 0 issued when more than one PDB file is open does not execute 
> model *
> 
> -- 
> 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
> 
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

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Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

2015-12-13 Thread trematodeo 
Hi Bob,

I need to ask because it's still confusing to me, the problem with the new
chrome version is when you drag - rotate - some model on the screen using
the mouse?

I updated my chrome and that's the problem I'm facing in my page. The model
rotation isn't smooth anymore.

To fix I need to update to the last jmol version?

I don't know about the chrome internals but seems to be a bad decision from
google, I'm glad that you have found a way to fix this, thanks.


Best regards
Fausto



On 13 December 2015 at 14:05, lisensky  wrote:

> I am getting a file not found for
> (fixed) http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm
>
> Did you post it?
>
> Thanks for working on this Chrome issue?
>
>
> --
> George Lisensky lisen...@beloit.edu
> Chemistry Department608-363-2225
> Beloit College  fax 608-363-2052
> 700 College Street
> Beloit, WI 53511
>
> http://chemistry.beloit.edu/classes/lisensky
>
>
>
> --
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Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

2015-12-13 Thread lisensky 
I am getting a file not found for
(fixed) http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm

Did you post it?

Thanks for working on this Chrome issue?


-- 
George Lisensky lisen...@beloit.edu
Chemistry Department608-363-2225
Beloit College  fax 608-363-2052
700 College Street
Beloit, WI 53511

http://chemistry.beloit.edu/classes/lisensky


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Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

2015-12-13 Thread Robert Hanson 
[slight correction]


(fixed) http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
(original) http://chemapps.stolaf.edu/jmol/jsmol-2015-12-13/jsmol.htm

On Sun, Dec 13, 2015 at 12:56 PM, Robert Hanson  wrote:

> This new version is now available at SourceForge:
>
> *Download Jmol-14.4.1_2015.12.13-binary.zip (60.3 MB)
> *
>
>
> *IMPORTANT*: A very recent modification of Chrome makes Chrome unusable
> with all previous versions of JSmol, at least until sometime in January.
> The WebGL version of JSmol is not impacted.
>
> This appears to be the result of a well-meaning attempt by Chromium
> developers to enhance smooth scrolling of pages by lowering the priority of
> setTimeout calls. However, the unanticipated fallout of that change results
> in extremely rough rotation of models. You can follow the issue here:
> https://code.google.com/p/chromium/issues/detail?id=568725  Note that one
> of the last comments on Dec. 11 indicates that there indicates this issue
> will not be addressed until sometime in January.
>
> *But there is a workaround. *This release of Jmol 14.4.1 should correct
> that problem and, at the same time, may improve performance with Microsoft
> Edge.
>
> I have put up two versions of JSmol that illustrate the problem and the
> fix:
>
> (original) http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
> (fixed) http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm
>
> Testing of that second site would be appreciated.
>
> The work-around is simple, and if you want, you can implement this
> yourself on your site.  Really (in terms of this bug) it is just a single
> coding change in jsmol/js/JSmol.js, where one "setTimeout(f)" has been
> replaced with "requestAnimationFrame(f)". Thus, if you prefer, you should
> be able to just swap in a new JSmol.min.js or JSmol.min.nojq.js for the old
> one. I have not tried this. Of course, if you do that, then the other bugs
> listed below will still be there. If you want to try that, here is the link
> to that file specifically:
>
> http://chemapps.stolaf.edu/jmol/jsmol2/JSmol.min.js
>
> Bob
>
> Jmol.___JmolVersion="14.4.1_2015.12.13"
>
> bug fix: JavaScript Chrome/Edge fix for slow response due to setTimeout
> issues; uses requestAnimationFrame instead in JSmol.js
> bug fix: zoomTo not setting time to 0 in the case of scriptWait
> bug fix: set selectAllModels should restrict action of display/hide as well
> bug fix: set selectAllModels not working appropriately
> bug fix: set selectAllModels should not be saved in state
> bug fix: JmolData.jar does not update atom screen positions upon REFRESH
> or select {visible}
> bug fix: JmolData.jar -p flag does not work properly
> bug fix: model 0 issued when more than one PDB file is open does not
> execute model *
>
> --
> 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
>
>


-- 
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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[Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT

2015-12-13 Thread Robert Hanson 
This new version is now available at SourceForge:

*Download Jmol-14.4.1_2015.12.13-binary.zip (60.3 MB)
*


*IMPORTANT*: A very recent modification of Chrome makes Chrome unusable
with all previous versions of JSmol, at least until sometime in January.
The WebGL version of JSmol is not impacted.

This appears to be the result of a well-meaning attempt by Chromium
developers to enhance smooth scrolling of pages by lowering the priority of
setTimeout calls. However, the unanticipated fallout of that change results
in extremely rough rotation of models. You can follow the issue here:
https://code.google.com/p/chromium/issues/detail?id=568725  Note that one
of the last comments on Dec. 11 indicates that there indicates this issue
will not be addressed until sometime in January.

*But there is a workaround. *This release of Jmol 14.4.1 should correct
that problem and, at the same time, may improve performance with Microsoft
Edge.

I have put up two versions of JSmol that illustrate the problem and the fix:

(original) http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
(fixed) http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm

Testing of that second site would be appreciated.

The work-around is simple, and if you want, you can implement this yourself
on your site.  Really (in terms of this bug) it is just a single coding
change in jsmol/js/JSmol.js, where one "setTimeout(f)" has been replaced
with "requestAnimationFrame(f)". Thus, if you prefer, you should be able to
just swap in a new JSmol.min.js or JSmol.min.nojq.js for the old one. I
have not tried this. Of course, if you do that, then the other bugs listed
below will still be there. If you want to try that, here is the link to
that file specifically:

http://chemapps.stolaf.edu/jmol/jsmol2/JSmol.min.js

Bob

Jmol.___JmolVersion="14.4.1_2015.12.13"

bug fix: JavaScript Chrome/Edge fix for slow response due to setTimeout
issues; uses requestAnimationFrame instead in JSmol.js
bug fix: zoomTo not setting time to 0 in the case of scriptWait
bug fix: set selectAllModels should restrict action of display/hide as well
bug fix: set selectAllModels not working appropriately
bug fix: set selectAllModels should not be saved in state
bug fix: JmolData.jar does not update atom screen positions upon REFRESH or
select {visible}
bug fix: JmolData.jar -p flag does not work properly
bug fix: model 0 issued when more than one PDB file is open does not
execute model *

-- 
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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