Protein Database Downloader

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.

Replies to This Discussion

Permalink Reply by Nik Willmore on February 24, 2016 at 4:09pm

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:

Attachments:

PDB E STICK MESH PIPES ONLY.gh, 24 KB
PDB D COCCON STICKS ONLY.gh, 41 KB

Permalink Reply by mark zirinsky on February 24, 2016 at 6:11pm

Neat work Nik, ABI will be jealous.

Permalink Reply by Nik Willmore on March 3, 2016 at 6:51pm

Who is ABI?

Permalink Reply by mark zirinsky on March 3, 2016 at 8:22pm

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

Permalink Reply by Tim on February 25, 2016 at 9:19pm

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

Awesome work.

Permalink Reply by Nik Willmore on February 27, 2016 at 3:41pm

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

Permalink Reply by Tim on February 27, 2016 at 7:40pm

))) 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

Permalink Reply by Nik Willmore on February 27, 2016 at 9:30pm

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.

Permalink Reply by Tim on February 27, 2016 at 9:37pm

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

Permalink Reply by Nik Willmore on February 28, 2016 at 11:51am

Trained as a chemist, now indeed a hobby.

Permalink Reply by Tim on February 28, 2016 at 7:43pm

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?

Permalink Reply by Nik Willmore on February 28, 2016 at 9:49pm

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!