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 <paulpil...@gmail.com> 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
> <https://github.com/biasmv/pv>
>
> - 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
> <https://github.com/dsehnal/LiteMol>
>
> - Molmil, is another open source viewer, used by PDBj. Demo here
> <http://gjbekker.github.io/molmil/> and github repo here
> <https://github.com/gjbekker/molmil>
> 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 <hans...@stolaf.edu> 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 <paulpil...@gmail.com> 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 <angel.herr...@uah.es> 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 don’t hang the web browser during the computation).
> Display most common bio-molecular representations, labels, select and color
> abilities.
>
> - NGL : documentation
> <http://arose.github.io/ngl/doc/#User_manual/Introduction/Welcome>
> NGL viewer demonstration http://proteinformatics.charite.de/
> ngl/html/ngl.html
> Article in Nucleic Acid Research :http://nar.oxfordjournals.
> org/content/early/2015/04/28/nar.gkv402.full
> Github Repo : https://github.com/arose/ngl
> Made by Alexander Rose, a contributor to this list ! Has probably the most
> beautiful graphic capabilities. Many bio-molecular representations (some
> unknown to me such as « hyperballs » and « ropes » ). Abilities to act on
> selections with a jmol-like syntax.
>
> - PV : http://biasmv.github.io/pv/
> GitHub repo : https://github.com/biasmv/pv
> Protein Viewer is used by SwissModel and RCSB. It has a very clear
> documentation <http://pv.readthedocs.org/en/latest/intro.html>. Graphics
> are stylized but also really clear in their depiction. Common bio-molecular
> representations are available. Selections are based on javascript and a
> JSON syntax.
>
> - Chemdoodle web components
> Examples <https://web.chemdoodle.com/demos/iza-zeolite-explorer/>
> Handles bimolecular representations and has some capabilities to handle
> cif files and generate multiple cells. Viewer canvases can be linked to a
> range of different widgets (spectrum display, 2D formula, etc…). Selection
> and display is based on the manipulation of javascript objects.
>
> - GLmol http://webglmol.osdn.jp/index-en.html
> might have been the first WebGL viewer available. Some of its code has
> been used in the JSmol WebGL front end experiment. Active development has
> apparently ceased.
>
> I have found some references to other viewers
> <https://www.snip2code.com/Snippet/579547/WebGL-based-protein-Viewers> in
> an informative page written by another Jmol contributor, Andreas Prlic
>
> To my knowledge, JSmol is the only one with such advanced computing
> capabilities (secondary structure determination, hydrogen & h-bonds
> calculation, molecular minimization, partial charges, electrostatic
> potential, etc…), displaying versatility (bio/geo/nano/chemistry, file
> formats diversity and oddities), and user interaction openness (picking,
> building, computing…).
>
> All these viewers seem more reactive to user interaction (at least on my 6
> years old laptop), even with high rendering quality settings. My
> understanding is that WebGL is the reason for this improvement (it might
> also be some other software complexity related concerns, I realize that I
> am not comparing the same things). I also understand that there is no plan
> for a development of Jsmol WebGL capabilities at the moment. Theoretically
> speaking, is it nonetheless feasible to harness JSmol capabilities to one
> of these viewers, in other words having JSmol doing all the computation
> while another library is doing all the GUI related business ?
>
> -Paul
>
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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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