Grasshopper

algorithmic modeling for Rhino

The PDB plug-in was rather inconvenient in requiring your to manually download Protein Database Files and it lacked an atom radius output, so I discovered Python has a built-in http download library, and I added atomic radii from Wikipedia.

The new Cocoon marching cubes plug-in along with Kangaroo MeshMachine to refine the mesh better than the native tweaky Cocoon refine component are included.

The smaller example takes about 15 seconds. The huge one a minute or two.

Just enter the PDB symbol, and you can browse for those here:

http://pdb101.rcsb.org/motm/motm-by-title

The small one above is a DNA repair enzyme wrapped around DNA:

http://www.rcsb.org/pdb/explore.do?structureId=3UGM

Some are just too big to test and will likely blow up Cocoon or at least MeshMachine.

I thought these structures might be useful to 3D printer enthusiasts looking for fun blobby shapes to build with.

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Same script, with ball-and-stick output via Grasshopper, with render color baking:

This overall is quite a bit slower compared to a single mesh outer contour that hides the incredible atomic complexity inside where most of the atoms exist.

Perhaps it could be converted into a single mesh with vertex colors but then you would lose the sharp color edges.

The Keyshot renderer groups them by color so you can change them rationally by just drag and drop.

Even my iPhone can render ball and stick in seconds with nice sharp shading (app = iMolview) so this is nowhere near as useful as the above surfacing technique.

Just bonds are more interesting, I imagine. Ah, and these could also be done more efficiently as a single Cocoon mesh using fat metalines! It's a bit slow but worked. Hard to see what's there without Keyshot's velvet fabric. You can see DNA popping out of the top here.

Since the bond wires are so well behaved and orderly, Exoskeleton ought to work too, the component called ExoWireframe, but it just won't work (boilerplate "object reference" error). I can isolate it to single pairs of lines at near right angles. Just a bug.

Just no atoms and round capped mesh pipes works:

 

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Neat work Nik, ABI will be jealous.

Who is ABI?

Applied Biosystems, division of Thermo Fisher, make peptide synthesizers, DNA sequencers, protein analyzers and other analytical equipment. Your visualizations are better than what they have

I'm a simple man, I see a blobby thing - I like. XD

Awesome work.

These be the micromachines we are all made of, including our thinking brains.

))) I know, the complexity amazes me, yet it all works, I wish I could see it live under an atomic microscope. But blobby representation should be pretty close.

https://www.youtube.com/watch?v=yqLlgIaz1L0

Transmission electron  microscopes are now routinely seeing macromolecules, here being a virus connector:

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2820/analysis

 Given the sequence information from the genetic code, it's easier for them to  then fit that into the blobby 3D structure to "solve" it.

Really awesome, are you working on the visualisation or is it more like a hobby?

Trained as a chemist, now indeed a hobby.

Awesome, with all the resources available on the web now, I sometimes think how amazing it would be for chemistry teachers in schools to use these tools and resources to show the molecules and atoms during the class. I would like to see your stuff as complexity examples when I was a pupil.

My classes were mostly lame and tasteless, teachers never used any media and we didn't have projectors in our classrooms. 

So I really appreciate all this cool awesome stuff on the internet, I leaned a lot from the teachers on the web, what my teachers couldn't explain with their words and books.

Do they all (proteins) tend to be symmetric or it is for the showcase?

I've personally been collecting the symmetrical ones for years on my little iPhone app iMolview.

Here's the PDB entry for the ring thing:

http://www.rcsb.org/pdb/explore.do?structureId=3j1w

And the various views on iMolview:

The alpha-helix and beta-sheet visual format is quite simplifying!

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