Sunday, December 6, 2009

The future of scientific publishing is here today

I recently came across this paper on embedding interactive 3D graphics in pdf files. Unfortunately, I couldn't animate the 3D figures, and I wrote the author (Vlad Vasilyev) who kindly wrote back that:

(1) the publisher (Springer) is a bit behind the times so the interactive figures are found in the supplemental material, but

(2) the ACS is more on the ball, as can be seen in this paper (this is the one I use in the screencast), and

(3) he has made a bunch of tutorials on how to create such diagrams on this page.

This page also contains some pdf files with 3D graphics you can play around with if you don't have access to the papers. Be sure to use Adobe Acrobat Reader 9.

Note that it is also possible to include animations such as vibrational motion (NB: 16 MB file)

Very cool! I haven't tried this myself, but you can be sure I will. Unfortunately, it seems that you need a piece of commercial software (Adobe Acrobat 9 Pro Extended) to do this.

On a related note, check you the interactive figure of interactive figures created by fellow blogger Henry Rzepa (please give the page some time to load).


NUChem said...

That is so cool.

Jan Jensen said...

Isn't it? Definitely the way of the future. Too bad there is no free software solution yet.

David Watson said...

Actually, you can embed movies and audio into pdf produced by LaTeX using the movie15 package. You might ask some of your mathematician colleagues about the use of LaTeX, or install MacTeX 2009 from (I assume from one of the screencasts you are using an Apple computer). There is a good introduction in the help menu of the program TeXShop to get you on your way.

Jan Jensen said...

David - interesting. Do you have an example of the finished product? Do you know if one can insert interactive graphics?

David Watson said...

Here is a 3D object exported to U3D via meshlab, and then included in a pdf through the use of LaTeX with the movie15 package:

Jan Jensen said...

David - excellent, thank you! I'll have to try this with a molecule. If anyone beats me to it, please add a comment.

David Watson said...

I was able to export an idtf file from a GAMESS file that I had imported into Jmol. I then used IDTFConverter to make a u3d file from the idtf. The u3d file could successfully be incorporated into a pdf file using the movie15 package and LaTeX.

Altogether, I must say that I'm not happy with all of the hoops that I had to jump through to make it work, nor the quality of the results, but if you want to see a sample file, I suppose I could email it to you.

I think the state of 3D, especially in pdf, is just not user-friendly enough to make this a priority for most researchers.

Jan Jensen said...

David - that was fast, thank you again!

I would very much like to see the result, so please email it to me ( Do you mind if I make it available for download?

I agree with you on the hoops business. Perhaps the first step is to ask Robert Hanson to add a u3d export option to Jmol?

Jan Jensen said...

Thanks for the file David.

Meanwhile, google has brought some new info to light.

1. Instructions for creating an IDTF file in Jmol can be found here.

2. The IDTF converter can also be compiled on Mac and Linux (here).

3. Robert Hanson has been hard at work on the U3D issue, and there might be an all java solution soon (here).

Jan Jensen said...

Here is the latest word in this from Mr Jmol

Anonymous said...

I wouldn't be as pessimistic as Mr Jmol is (was?). The documentation of the movie15 package describes how to define the camera and object positions, so you have to play with that. There is also the possibility of including some javascript file to modify a bunch of settings. All in all, I agree that it isn't particularly user friendly (unless you are prepared to pay for Acrobat Pro), but we are talking about a very specialised application.

By the way, I couldn't make to work any of the U3D files generated by Meshlab, so I had to resort to alternatives and found the excellent package jReality. You may want to check it out, the U3D export function works well and there is a tutorial with a javascript example that automatically calculates the camera settings based on the bounding box of your model. It shouldn't be difficult to get what you want if you align your molecule alongside the axes.

Jan Jensen said...

Anonymous - thanks very much for the update. Yes, jReality sounds like a good alternative, especially if one could get a direct interface to Jmol (see this interesting discussion).

Mr Jmol recently suggested an interesting alternative. Smaller files and easy to make, but not quite as cool as interacting with the figure within the pdf file.

My current thinking is that it is perhaps better to switch to something like the epub format. It's basically html but can be made to look as nice as pdf, and there are many cool epub readers out there. The html aspect should make it possible to embed Jmol....?

Troels Schwarz-Linnet said...

Hi Jan.

In PyMOL, it now easy to save your protein in IDTF format, which (kind of easy) can be converted to U3D format -> Ready for implementing in LaTeX through the media15 package.

That makes a .pdf with your protein you can zoom around in. As for now, it seems you only can export to cartoon format, no sticks yet.

Read more here, and see example:

Jan Jensen said...

Hi Troels

Thanks for that!