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 http://slurl.com/secondlife/SBU%20Medical%20Center/58/26/28.

A visit to the monolith...

Imagine being able to fly through a molecule. Well now you can at the Stony Brook School of Medicine SL site where Erich Bremer has put together Monolith. Monolith creates huge complex molecules using a complex Second Life script that is actually able to import data from some of the standard molecular data base files and use that data to create 3D molecules. Way cool!

Here is monolith itself. Straight out of 2001 at the Stony Brook site.




Some molecular views. I made these a little bit dramatic and I bet some of the more artistic SL residents will want to visit.

This is a transfer RNA.














And to show you the scale these models are done at, in this view I am barely visible on the left hand side of the image:
















One more view. The metallic looking molecule in the foreground is DNA.


This is a really neat system. I haven't had a chance to play with monolith and the program is still under development.

One weakness of course is that each atom is a single prim. So that tRNA might gobble up 400 prims...so if you don't own an island monolith probably won't work. It might be possible to save on prims if monolith can be pre programmed with certain stock sculpted prims for certain common structures, but suspect it is not practical.



Certainly monolith would not work on my land in Carmine...let's see (teleporting home for a sec), one of my parcels is 1024 m squared and it supports 234 prims. Even the Stony Brook land (teleporting back...) supports roughly 15,000 prims...so Monolith could quickly eat into that. So Linden lab...if you want SL to be able to host these intensive sort of educational environments, we need more prims!

If you have SL installed on your machine visit Monolith at

http://slurl.com/secondlife/SBU%20Medical%20Center/58/26/27