For a 3D data rendering, I used the VMD modeling software to visualize the POPC lipid membrane and water molecules, which are covering the surfaces of two lipid leaflets.
I believe, with VMD you got the right software. Alternatives highly depend on your task with your data. Even for "pretty pictures" I recommend the tachyon ray tracer of VMD (http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/).
If you are in need of interactive high-performance visualization (due to the size of the data set) you might want to look into research prototypes like Qutemol (rather old: http://qutemol.sourceforge.net/) or MegaMol (my own tool for my PhD-Student-Days, which is cutting-edge fast but a pain to set up and to use: http://www.sfb716.uni-stuttgart.de/forschung/software/megamol.html). There are, of course, many other tools like these out there. You could also look into the commercial sector, like Amira (http://www.vsg3d.com/amira/molecular) or Autodesk's Maya Molecular Toolkit (http://blogs.oregonstate.edu/inspire/2012/12/12/molecular-maya-toolkit-a-powerful-visualization-add-on-for-autodesk-maya/). But I never really worked with one of these commercial tools.
So, long story short: "the best" software highly depends on your task, and VMD is really powerful.
Actually, these pictures were done with the Tachyon ray tracer of VMD. As you may see, the results are quite ok. At the beginning, I used the Maya molecular toolkit (Autodesk), but this software is cumbersome and very hard to operate. It might be the only choice for high-quality 3D movies with astonishing visual effects though.
I also found that VMD to be very useful for visualizing molecular dynamics
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