Friday, January 16, 2009

Molecular Mayhem in Second Life

Yesterday I visited with Erich Bremer from Stony Brook for a quick tour of Monolith, his Molecular rezzer, discussed in my previous post. He asked me to select a protein from the Protein Data Base(RCSB) so he could test it on his new beta version of Monolith. So many proteins! So I picked three favorites, a cytochrome C (pdb 3CP5), a dicer (2FFL) and a Rubisco (1RXO). The dicer and Rubisco would have required too many prims for the sim-I should have known that- but we had lots of fun rezzing and playing with cytochrome C.

Two big things. First Monolith is fast. It takes roughly one minute to rez a protein. Since a protein such as cytochrome C easily has 5,000 plus atoms, each of which is rezzed as a prim.

Second Monolith provides a fair amount of flexibility to color different regions of the molecule. For instance, cytochrome C has a heme group-this is a set of four carbon rings with an iron atom in the middle, just as in hemoglobin. Erich was able to immediately find the heme group in the pdb format file and color it, just as one might do with a traditional molecular rendering tool such as Cn3D.

Right now Monolith only does space filling models but Erich has plans for ball and stick models, and some ideas for clever use of particles. Monolith is not nearly as powerful as s Cn3D in terms of the types of displays you can use and right now you can't rotate the molecule right now and scaling might be nice, but then these traditional viewers don't let you easily fly through the molecule.

Not quite the holy grail of molecular rendering which for me would be a Cn3D type rendering system in world. But given that Monolith is still in beta, it's pretty impressive given the current constraints of Second Life's environment the Erich has to work around.

Monolith is at


Hiro Sheridan said...

Cool snapshots. Is he planning to release monolith to the SL community?

If you're interested in rezzing proteins, I would recommend Peter Miller's protein rezzing toolkit that allows for space filling, stick and ball, coloring, particles, etc. Also allows for the packaging and rotation of proteins, even if the number of prims is over 255 (which it usually is), see: here and here. Single prim proteins can also be rezzed.

Peter also has lots of other biology in SL stuff that you may be interested in.

Simone said...

Thanks Hiro, we'll check this out!