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Avogadro, GLSL and X-Ray Vision

Posted by Marcus D. Hanwell on

My regular readers may remember I talked about the GLSL shaders I was adding to Avogadro. I got my head around GLSL, uniform variables and the loading process. I also raided Molekel for some nice shaders. Ever since I first saw the X-ray screenshot I have loved it. I am very pleased to announce I now have this working in Avogadro!

Avogadro, GLSL and X-Ray Vision Avogadro, GLSL and X-Ray Vision with Colour

I will give you a moment to bask in the beauty. It is a really nice visual that helps you to really see what is happening with many surfaces. The image on the left is the classic, as Mario Valle introduced it, along with other great work he has done in the area of molecular visualisation. I was lucky enough to meet him earlier this year at a conference and discuss a few ideas with him.

Tpy-Co-S with GLSL rendered HOMO

There are still a few rough edges with the new GLSL code. I hope you agree that the results are quite stunning, I really liked this final image too.

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Benoit Jacob on :

Benoit JacobIncredible!
Now I have to get my nvidia card working again... is switched back to the intel graphics as they give better performance than the nvidia 7400 with KDE 4 but i'll have to check out the latest drivers...

One suggestion about your blog, the images appear scaled (using firefox 3.0) which make them look not as good as if they were shown at the actual size.

Marcus D. Hanwell on :

Marcus D. HanwellThanks for the suggestion, I am using Firefox 3 and it looks fine here. I am using scaled down thumbnails in the entry with links to the full size image.

Hopefully this new functionality will be useful, it has certainly been very interesting learning about GLSL and shaders in general.

Benoit Jacob on :

Benoit JacobI can see that; there is of course nothing wrong about scaled-down thumbnails; now I just realized that my problem is that I had enabled zoom in firefox and so the thumbnails were zoomed-in. I'm not 100% convinced that this new feature, zooming everything instead of just text, is always a good thing....

Peter on :

PeterHi Marcus,

the work on Avogadro is really impressive. I used it lately to draw some molecules for a poster.
I definitely have to tell my colleagues at the chemistry department about it. I think it will come handy for some researchers and of course for students. When do you expect the next release?

Kind regards
Peter

Marcus D. Hanwell on :

Marcus D. HanwellI am glad to hear you have found it useful. I am hoping that we will be able to make a release some time this month, I know that we could still do with releasing much more often.

I have been doing a lot of work in the core of Avogadro in order to increase stability and open up the possibility of Python scripting in a meaningful way. This work has gone quite well but I would like to get some of the old plugins ported before making a release.

I will certainly announce it on here once we do.

Peter on :

PeterI think your "release cycle" is okay. I was just wondering because I want to give my colleagues your tool in the best shape.
My sound like a stupid question but is there any peer-reviewed paper about Avogadro?

Geoffrey Hutchison on :

Geoffrey HutchisonPeter,

We haven't published a paper on Avogadro, simply because the program isn't really in a "finished" state. Yes, the early results are very promising. ;-)

Our intention is to clean up some loose bits for a 0.9 and 1.0 release while we write the manuscript. If you have suggestions about journals (i.e., the best audience), we'd definitely be receptive.

Peter on :

PeterIf it would be a biology tool I would suggest PLoS but chemistry is not my core business (as mentioned I just used it for some simple molecules). I will ask my colleagues from the chemistry department what they think (though I suppose they won't have a good suggestion either).

Regards
Peter

Marcus D. Hanwell on :

Marcus D. HanwellI am glad you feel the release cycle is OK, I would still prefer for us to get releases out a little more often. This particular cycle has been quite different due to some of the major rewrites happening in a trunk.

As Geoff said, we are hoping to get a peer-reviewed paper out in the 0.9/1.0 timeframe. I would like to make a 0.9 alpha once we have the basic features working again. Hopefully we can get feedback on the releases quite quickly in order to release version 0.9.

Peter on :

PeterTo use a simple phrase. It's finished when it's finished. I think this says all.

Anyways, I'll no longer distract you with my silly post from coding on Avogadro. ;-)

Keep up the good work. I'm looking forward to see new screen casts.

Ted on :

TedCan this enhanced visualization lead to new discoveries or is it purely educational? Very good work btw.

Marcus D. Hanwell on :

Marcus D. HanwellThat is a tough question... In all honesty I think that as a researcher, having tools available such as Avogadro can facilitate new discoveries, although I doubt it will lead to them directly on its own. As with most research tools they are necessary to do research and make great discoveries in the right hands.

Most of us who are involved in Avogadro development felt quite passionately that the research world needed a good, flexible open source tool for computational chemistry. I think that Avogadro has the potential to become that tool. Due to the plugin based nature of the code and the new Python scripting support it is possible to do things with Avogadro that are not possible in other less flexible tools.

I think Avogadro is suited to helping both researchers and educators.

baoilleach on :

baoilleachIf you're going to be talking about X-ray vision, you should be showing the electron density instead. Square that wavefunction immediately!! :-)

Marcus D. Hanwell on :

Marcus D. HanwellSorry for the delay - I squared it now... We were busy working on the interface, Python bindings and optimising for big systems ;-)

New and improved webcast to follow with X-rays, electron density and lots of pretty colours!

Perspektive Scheidung on :

Perspektive ScheidungCongratulations.

I have been visiting your site a few times recently and I like the way you write about things, you have a very interesting perspective. Good things.

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