Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

[Angel Herráez]

Of interest on this topic, this article has just been published:

Implementing WebGL and HTML5 in Macromolecular Visualization and 
Modern Computer-Aided Drug Design
Shuguang Yuan, H.C. Stephen Chan, Zhenquan Hu
https://doi.org/10.1016/j.tibtech.2017.03.009



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Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

[Robert Hanson]

I note that one could connect JSmol to any of these with only a little
work. Just hasn't been done.

On Mon, May 15, 2017 at 1:33 PM, Paul PILLOT  wrote:

> Dear Jmolers,
> the original message of this thread was posted one year and a half ago…
> and discussed about libraries using WebGL to display macromolecules.
>
> Since then, the landscape of webGL molecular viewers has reshaped:
> - PV is now in maintenance mode : "This project is currently in
> maintenance mode. I simply just don't have the time to work on it anymore.
> I'm happy to fix smaller bugs and answer support requests, though it might
> take a while until I can answer those. » from github repo
> 
>
> - chemDoodle webcomponents has not been updated since nov 2015
>
> - 3dmol.js and NGL (see original post below) are still actively developed
> and from the activity on their respective github accounts are gaining
> contributors and tractions
>
> - Litemol is another opensource viewer (written in typescript) :
> https://webchemdev.ncbr.muni.cz/LiteMol/
> it’s used by PDBe. The githug repo is here
> 
>
> - Molmil, is another open source viewer, used by PDBj. Demo here
>  and github repo here
> 
> Article for reference : https://jcheminf.springeropen.com/articles/10.
> 1186/s13321-016-0155-1
> It uses a subset of Pymol’s command language
>
> -Paul
>
> Le 03-11-2015 à 16:05, Robert Hanson  a écrit :
>
> And don't forget that Jmol has a WebGL option, but I don't claim that it
> is any better than the others. It's not our forte, and it comes with a
> significant overhead if all you want is a molecule to show.
>
> On Tue, Nov 3, 2015 at 1:57 PM, Paul PILLOT  wrote:
>
>> Hi Angel,
>> feel free to include this comparison in the wiki for further reference.
>>
>> I fully agree with all your comments. Persistency of web libraries is an
>> important aspect.
>> Some are funded projects (3Dmol.js relies on a grant), some are academic
>> or backed by
>> public institutions. Open source development (such as public source
>> repositories) provide
>> an opportunity for future developments.
>> The ease of implementation of the library should also be taken into
>> account, especially if
>> you’re going for a multiple alternatives option.
>>
>> Vive Jmol !
>>
>>
>> > Le 03-11-2015 à 04:45, Angel Herráez  a écrit :
>> >
>> > Hi Paul
>> >
>> > Thank you for the information, it is very interesting. I had already
>> seen PV in
>> > action, but not others. I wonder how much hard work is being duplicated
>> in
>> > parallel.
>> >
>> > I'm quite sure that the better performance is due to WebGL, not to the
>> > efficiency of the software code.
>> >
>> > The old problem with WebGL was lack of support in old machines (graphic
>> > cards). I guess this is a nearly negligible worry today --though I
>> wonder about
>> > tablets.
>> >
>> > Another big issue is permanence; many programs are "experiments" that
>> > quickly go dead. I have not experienced this with 3D, but It happened
>> with
>> > 2D molecule drawing, very nice and promising ones stopped being
>> > developed. See http://biomodel.uah.es/en/DIY/
>> > http://biomodel.uah.es/en/DIY/comparison.htm
>> >
>> > That is worrisome when trying to choose.
>> >
>> > But anyway your comparison is very useful and one could design pages
>> > offerring altenatives to users, as e.g. RCSB is now doing: PV / JSmol /
>> > JmolJava
>> >
>> > If you don't mind, I'd be happy to add your comparison table to the Jmol
>> > Wiki, so we can easily find it and keep if updated.
>> >
>> > And finally, I wish some of the "expertise" of these programs would
>> entice
>> > someone to step ahead and grab the task of further implementing WebGL in
>> > Jmol (I'm not saying Bob Hanson)
>> >
>> > Long live Jmol!
>> >
>> >
>>
> Original post :
> Dear Jmolers,
> with the end of Java embedded plugins, we are now relying on JSmol for
> displaying molecular structures in web pages.
> If JSmol bio/geo/chemicabilities appear to me as limitless, I am
> encountering other limitations in respect with its performances : some web
> applications I made are particularly slow even if tuning is possible to
> some extent. This is why I took a look at the alternatives currently
> flourishing on the web which rely on WebGL to display the 3D scenes in the
> browser. None of them could be considered as a replacement to JSmol for my
> purposes, but I thought it could be interesting to share my findings with
> the list.
>
> - 3Dmol.js : http://3dmol.csb.pitt.edu/index.html
> Article in PMC : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393526/
> Github Repo : https://github.com/3dmol/3Dmol.js
> Has the simplest embedding mechanisms I have ever seen, based on HTML
> markup or url formatting. Abilities to compute isosurfaces in parallel (use
> web workers that 

Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

[Paul PILLOT]

Dear Jmolers,
the original message of this thread was posted one year and a half ago… and 
discussed about libraries using WebGL to display macromolecules.

Since then, the landscape of webGL molecular viewers has reshaped:
- PV is now in maintenance mode : "This project is currently in maintenance 
mode. I simply just don't have the time to work on it anymore. I'm happy to fix 
smaller bugs and answer support requests, though it might take a while until I 
can answer those. » from github repo 

- chemDoodle webcomponents has not been updated since nov 2015

- 3dmol.js and NGL (see original post below) are still actively developed and 
from the activity on their respective github accounts are gaining contributors 
and tractions

- Litemol is another opensource viewer (written in typescript) : 
https://webchemdev.ncbr.muni.cz/LiteMol/ 

it’s used by PDBe. The githug repo is here 

- Molmil, is another open source viewer, used by PDBj. Demo here 
 and github repo here 
 
Article for reference : 
https://jcheminf.springeropen.com/articles/10.1186/s13321-016-0155-1 

It uses a subset of Pymol’s command language

-Paul

> Le 03-11-2015 à 16:05, Robert Hanson  a écrit :
> 
> And don't forget that Jmol has a WebGL option, but I don't claim that it is 
> any better than the others. It's not our forte, and it comes with a 
> significant overhead if all you want is a molecule to show.
> 
> On Tue, Nov 3, 2015 at 1:57 PM, Paul PILLOT  > wrote:
> Hi Angel,
> feel free to include this comparison in the wiki for further reference.
> 
> I fully agree with all your comments. Persistency of web libraries is an 
> important aspect.
> Some are funded projects (3Dmol.js relies on a grant), some are academic or 
> backed by
> public institutions. Open source development (such as public source 
> repositories) provide
> an opportunity for future developments.
> The ease of implementation of the library should also be taken into account, 
> especially if
> you’re going for a multiple alternatives option.
> 
> Vive Jmol !
> 
> 
> > Le 03-11-2015 à 04:45, Angel Herráez  > > a écrit :
> >
> > Hi Paul
> >
> > Thank you for the information, it is very interesting. I had already seen 
> > PV in
> > action, but not others. I wonder how much hard work is being duplicated in
> > parallel.
> >
> > I'm quite sure that the better performance is due to WebGL, not to the
> > efficiency of the software code.
> >
> > The old problem with WebGL was lack of support in old machines (graphic
> > cards). I guess this is a nearly negligible worry today --though I wonder 
> > about
> > tablets.
> >
> > Another big issue is permanence; many programs are "experiments" that
> > quickly go dead. I have not experienced this with 3D, but It happened with
> > 2D molecule drawing, very nice and promising ones stopped being
> > developed. See http://biomodel.uah.es/en/DIY/ 
> > 
> > http://biomodel.uah.es/en/DIY/comparison.htm 
> > 
> >
> > That is worrisome when trying to choose.
> >
> > But anyway your comparison is very useful and one could design pages
> > offerring altenatives to users, as e.g. RCSB is now doing: PV / JSmol /
> > JmolJava
> >
> > If you don't mind, I'd be happy to add your comparison table to the Jmol
> > Wiki, so we can easily find it and keep if updated.
> >
> > And finally, I wish some of the "expertise" of these programs would entice
> > someone to step ahead and grab the task of further implementing WebGL in
> > Jmol (I'm not saying Bob Hanson)
> >
> > Long live Jmol!
> >
> >
Original post :
Dear Jmolers,
with the end of Java embedded plugins, we are now relying on JSmol for 
displaying molecular structures in web pages.
If JSmol bio/geo/chemicabilities appear to me as limitless, I am encountering 
other limitations in respect with its performances : some web applications I 
made are particularly slow even if tuning is possible to some extent. This is 
why I took a look at the alternatives currently flourishing on the web which 
rely on WebGL to display the 3D scenes in the browser. None of them could be 
considered as a replacement to JSmol for my purposes, but I thought it could be 
interesting to share my findings with the list.

- 3Dmol.js : http://3dmol.csb.pitt.edu/index.html 

Article in PMC : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393526/ 

Github Repo : https://github.com/3dmol/3Dmol.js 

Has the simplest embedding mechanisms I have ever seen, based 

Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

[Robert Hanson]

JSmol -- Jmol/HTML5 Demo



On Wed, Nov 4, 2015 at 3:19 AM, Angel Herráez  wrote:

> El 3 Nov 2015 a las 15:05, Robert Hanson escribió:
> > And don't forget that Jmol has a WebGL option, but I don't claim that it
> is any better than the
> > others. It's not our forte, and it comes with a significant overhead if
> all you want is a molecule to
> > show.
>
> Yes, I am aware of that.
> Bob, I noticed there is a JSmol.GLmol.min.js  that needs to be called in
> addition to JSmol.min.js
> Is the order for calling those two important?
>
>
>
>
> --
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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] State of the world of WebGL "alternatives" to JSmol

[Angel Herráez]

El 3 Nov 2015 a las 15:05, Robert Hanson escribió:
> And don't forget that Jmol has a WebGL option, but I don't claim that it is 
> any better than the 
> others. It's not our forte, and it comes with a significant overhead if all 
> you want is a molecule to 
> show.

Yes, I am aware of that.
Bob, I noticed there is a JSmol.GLmol.min.js  that needs to be called in 
addition to JSmol.min.js
Is the order for calling those two important?



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Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

[Robert Hanson]

And don't forget that Jmol has a WebGL option, but I don't claim that it is
any better than the others. It's not our forte, and it comes with a
significant overhead if all you want is a molecule to show.

On Tue, Nov 3, 2015 at 1:57 PM, Paul PILLOT  wrote:

> Hi Angel,
> feel free to include this comparison in the wiki for further reference.
>
> I fully agree with all your comments. Persistency of web libraries is an
> important aspect.
> Some are funded projects (3Dmol.js relies on a grant), some are academic
> or backed by
> public institutions. Open source development (such as public source
> repositories) provide
> an opportunity for future developments.
> The ease of implementation of the library should also be taken into
> account, especially if
> you’re going for a multiple alternatives option.
>
> Vive Jmol !
>
>
> > Le 03-11-2015 à 04:45, Angel Herráez  a écrit :
> >
> > Hi Paul
> >
> > Thank you for the information, it is very interesting. I had already
> seen PV in
> > action, but not others. I wonder how much hard work is being duplicated
> in
> > parallel.
> >
> > I'm quite sure that the better performance is due to WebGL, not to the
> > efficiency of the software code.
> >
> > The old problem with WebGL was lack of support in old machines (graphic
> > cards). I guess this is a nearly negligible worry today --though I
> wonder about
> > tablets.
> >
> > Another big issue is permanence; many programs are "experiments" that
> > quickly go dead. I have not experienced this with 3D, but It happened
> with
> > 2D molecule drawing, very nice and promising ones stopped being
> > developed. See http://biomodel.uah.es/en/DIY/
> > http://biomodel.uah.es/en/DIY/comparison.htm
> >
> > That is worrisome when trying to choose.
> >
> > But anyway your comparison is very useful and one could design pages
> > offerring altenatives to users, as e.g. RCSB is now doing: PV / JSmol /
> > JmolJava
> >
> > If you don't mind, I'd be happy to add your comparison table to the Jmol
> > Wiki, so we can easily find it and keep if updated.
> >
> > And finally, I wish some of the "expertise" of these programs would
> entice
> > someone to step ahead and grab the task of further implementing WebGL in
> > Jmol (I'm not saying Bob Hanson)
> >
> > Long live Jmol!
> >
> >
> >
> >
> >
> --
> > ___
> > 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
>



-- 
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] State of the world of WebGL "alternatives" to JSmol

[Paul PILLOT]

Hi Angel,
feel free to include this comparison in the wiki for further reference.

I fully agree with all your comments. Persistency of web libraries is an 
important aspect.
Some are funded projects (3Dmol.js relies on a grant), some are academic or 
backed by
public institutions. Open source development (such as public source 
repositories) provide
an opportunity for future developments.
The ease of implementation of the library should also be taken into account, 
especially if
you’re going for a multiple alternatives option.

Vive Jmol !


> Le 03-11-2015 à 04:45, Angel Herráez  a écrit :
> 
> Hi Paul
> 
> Thank you for the information, it is very interesting. I had already seen PV 
> in 
> action, but not others. I wonder how much hard work is being duplicated in 
> parallel.
> 
> I'm quite sure that the better performance is due to WebGL, not to the 
> efficiency of the software code.
> 
> The old problem with WebGL was lack of support in old machines (graphic 
> cards). I guess this is a nearly negligible worry today --though I wonder 
> about 
> tablets.
> 
> Another big issue is permanence; many programs are "experiments" that 
> quickly go dead. I have not experienced this with 3D, but It happened with 
> 2D molecule drawing, very nice and promising ones stopped being 
> developed. See http://biomodel.uah.es/en/DIY/
> http://biomodel.uah.es/en/DIY/comparison.htm
> 
> That is worrisome when trying to choose.
> 
> But anyway your comparison is very useful and one could design pages 
> offerring altenatives to users, as e.g. RCSB is now doing: PV / JSmol / 
> JmolJava
> 
> If you don't mind, I'd be happy to add your comparison table to the Jmol 
> Wiki, so we can easily find it and keep if updated.
> 
> And finally, I wish some of the "expertise" of these programs would entice 
> someone to step ahead and grab the task of further implementing WebGL in 
> Jmol (I'm not saying Bob Hanson)
> 
> Long live Jmol!
> 
> 
> 
> 
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users


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