GLmol development and chemistry education (2012-04-28 19:55 by johannespernaa #63472)
Hi all.
Goog work with the GLmol software. This is an amazing software so far, but may I suggest some features that would be really important from the chemistry education point of view.
Are there any plans for the development of the electrostatic potential surfaces with color coding (transparent function also needed), and also better visualizations for the double and triple bonds are essential.
Ball & stick model is also important.
Best regards
Johannes
RE: GLmol development and chemistry education (2012-04-29 09:33 by biochem_fan #63479)
Thank you very much for comments.
For molecules loaded from SDF/MOL files, it is already possible
to draw double/triples bonds in "line" representation.
Do you want to visualize multiple bonds in "stick" representation, too?
"Ball & stick" is possible by giving different values for bondR and
atomR to drawBondsAsStick function.
The most difficult one is surface representation.
Although surface calculation is implemented in http://webglmol.sourceforge.jp/surface.html ,
as you can see, it is not very fast.
Electrostatic potential calculation is more demanding
and I have no idea how to implement it in Javascript.
However, I do have a plan to implement a viewer,
which can load colored surfaces precalculated by
other softwares (like Jmol).
RE: GLmol development and chemistry education (2012-04-30 02:56 by johannespernaa #63495)
Multiple bonds: Yes I tried double/triple bond visualizations in line mode, but they were really thin and line models in general are not so familiar to students. It would really be an important feature to if the multiple bonds could be visualized in ball & stick and stick modes too.
Ball & stick: Ok, thanks for the tip. I try this out.
Electrostatic potential surfaces: I think your solution will do the trick. From Jmol the surfaces can be exported for example as 3D models (X3D for example). Are these imported surfaces possible to be embedded to web pages too?
RE: GLmol development and chemistry education (2012-04-30 23:29 by biochem_fan #63509)
OK, I will implement the feature in the future update.
For the time being, you can increase bond width in "line" representation by
the 3rd argument of drawBondsAsLine function. You can also comine
"line" and "spheres" to make "ball and stick" representation.
(If you need examples, I will make. Just tell me so)
> I think your solution will do the trick. From Jmol the surfaces can be exported for example as 3D models (X3D for example). Are these imported surfaces possible to be embedded to web pages too?
I am considering JVXL, which is very compact.
However, it is difficult to implement, so please give me time.
RE: GLmol development and chemistry education (2012-05-22 19:31 by johannespernaa #63948)
Hi.
Thanks for the quick update.
I made some testing and I found that:
- I couldn't load Spartan calculated mol-file into the viewer
- Spartan calculated sdf-file loaded fine and the double bond visualizations look really impressive
- but with molecules with triple bonds (tested with acetonitrile) the triple bond visualization did not work using sdf-format
RE: GLmol development and chemistry education (2012-05-22 21:12 by biochem_fan #63949)
Hi,
Thank you very much for testing and giving me feedback.
> I made some testing and I found that:
> - I couldn't load Spartan calculated mol-file into the viewer
> - Spartan calculated sdf-file loaded fine and the double bond visualizations look really impressive
MOL/SDF reader seems not as good as PDB reader. I will improve it.
Could you please send me the files so that I can reproduce the bug?
You can paste it here or send by mail.
(biochem_fan at users dot sourceforge dot jp)
> - but with molecules with triple bonds (tested with acetonitrile) the triple bond visualization did not work using sdf-format
RE: GLmol development and chemistry education (2012-05-22 22:30 by johannespernaa #63951)
Yes, I send the files via e-mail.
By the way. I also downloaded and tested the NDKmol with my android phone. The touch pad navigation works really smoothly. Any plans to implement those touch pad navigation features to GLmol package?
I think they would be really handy when teachers are embedding models to their web pages. Students could visualize them via phones and tablets and so on. I think it would be easier for some teachers just to implement the molecules to web pages than ask students to download the software.
RE: GLmol development and chemistry education (2012-05-22 23:26 by biochem_fan #63954)
Hi,
Thanks for the sample files; I received them.
> it would give more information from the molecule, if hydrogen
> atoms are visualized a bit smaller than e.g. carbon atoms and the
> same for all atoms...
Does it suffice to scale sphere radius propotional to van der Waals
radius as in "spheres" representation?
It is easily implementable.
> The touch pad navigation works really smoothly. Any plans to implement those touch pad navigation features to GLmol package?
So you want to run GLmol (not NDKmol) on mobile platforms?
Well, that is what I wanted to do at the beginning, but
found possible only on limited devices.
GLmol depends on WebGL. Being relatively new technology,
WebGL is supported on only minor subset of mobile devices.
+ Sony Ericsson's Android phones support it.
GLmol works on them (confirmed).
+ Other Android devices doesn't support WebGL on standard
browser. However, Opera Mobile and Firefox Mobile support
WebGL. GLmol should work on them (not tested).
+ iPad & iPhone internally support WebGL, but Apple disabled it
for unknown (maybe political / strategic) reasons.
Many developers are pleading WebGL support.
Reportedly, newer version of Android will support WebGL by default.
For iOS, I have no idea.
RE: GLmol development and chemistry education (2012-05-23 02:15 by johannespernaa #63961)
> Does it suffice to scale sphere radius propotional to van der Waals
> radius as in "spheres" representation?
> It is easily implementable.
Yes, I think that it will work. And if the size difference is too big, it could be scaled down a bit using some kind of coefficient.
> GLmol depends on WebGL. Being relatively new technology,
> WebGL is supported on only minor subset of mobile devices.
Yeah, the number of devices is still limited but the future will change that, I hope.
I tried to refer the touchpanel support. My phone runs WebGL fine, but the touchpanel navigation is a bit sticky.
> I tried to refer the touchpanel support. My phone runs WebGL fine, but the touchpanel navigation is a bit sticky.
I see.
It is certain that GLmol should have UI designed for mobile devices.
However, I am afraid that I cannot improve it right now.
The problem is that, as far as I know, Android's browser doesn't
support multitouch events for Javascript.
In addition to this, my Android phone doesn't support WebGL,
Android Emulator neither.
RE: GLmol development and chemistry education (2012-05-22 23:55 by biochem_fan #63955)
OK, I examined your files.
> - I couldn't load Spartan calculated mol-file into the viewer
To my surprise, there are two completely different MOL formats!
What GLmol support is MDL's MOL and MDL's SDF format.
Spartan's MOL file is SYBYL's MOL format.
As the first seems more popular, I will not support the latter.
Please use SDF format to display the results from Spartan.
(I will update the document)
> - but with molecules with triple bonds (tested with acetonitrile) the triple bond visualization did not work using sdf-format
RE: GLmol development and chemistry education (2012-05-23 02:03 by johannespernaa #63960)
Aah, okay. So there is the difference.
I did not think that but now when you said it, I remember that there really is two diffrent mol-files.
I have worked with SYBYL mol2-file format in some animation project.
Yes but this is fine I can work with MDL MOL and spartan SDF files.
RE: GLmol development and chemistry education (2012-05-22 22:41 by johannespernaa #63952)
I also have one more design suggestion for the ball & stick model.
It seems that all atoms are visualized in the same size. From the educational point of view, it would give more information from the molecule, if hydrogen atoms are visualized a bit smaller than e.g. carbon atoms and the same for all atoms...
Would this kind of feature be possible to implement?
biochem_fan #63479)
