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/
<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
<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
> <mailto: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
> > <mailto: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/>
> > http://biomodel.uah.es/en/DIY/comparison.htm
> > <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
<http://3dmol.csb.pitt.edu/index.html>
Article in PMC : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393526/
<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393526/>
Github Repo : https://github.com/3dmol/3Dmol.js
<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
<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
<http://nar.oxfordjournals.org/content/early/2015/04/28/nar.gkv402.full>
Github Repo : https://github.com/arose/ngl <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/ <http://biasmv.github.io/pv/>
GitHub repo : https://github.com/biasmv/pv <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
<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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