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 28, 2016 at 11:43pm

Kinesin:

Permalink Reply by Kim hauer on February 28, 2016 at 1:34pm

I would like to think changing the DNA of our thinking brains might be the key to our Survival.

I was interested to learn 99 Million years ago 2 ants Supposedly were locked in mortal combat which was found in Burmese Amber.

http://news.discovery.com/animals/insects/ancient-ants-in-amber-wer...

Fast forward 99 Million years, and we are still kill each other, with our very own thinking brains! Nothing seems to have changed in 99 million years. Yet we have the audacity to think we now going to solve Global Warming? conveniently renamed Climate Change!

are you kidding me!

Permalink Reply by Tim on February 28, 2016 at 7:33pm

Just literally google "is world getting better" and check up some statistical data. Unless you are a conspiracy theory enthusiast XD, you will see that world is getting better, slowly but steadily.

Anyway, hope you find this info reassuring and believable (some people just enjoy boiling in the negativity) and have a good and productive day.

Permalink Reply by Mateusz Mazurek on April 16, 2016 at 10:21am

Hey, where can I download marching cubes components?

Permalink Reply by Nik Willmore on April 16, 2016 at 1:34pm

Cocoon:

http://www.bespokegeometry.com/2015/07/22/cocoon/

Permalink Reply by Ryan Hoover on April 18, 2016 at 12:17pm

This looks great, Nick. Thanks for sharing. You may also be interested in the suite of Grasshopper tools called "Alba" that I've just release for synthetic biology. It i

ncludes a component that allows you to search an amino acid sequence on RCSB, download the best match, and visualize the structure of the protein as a "ribbon" showing beta sheets and alpha helices. You can find more info and download it h ere.

Cheers,

Ryan

Permalink Reply by Nik Willmore on April 20, 2016 at 8:43am

Ribbons! Fun candy.

I'd also like to surface electron microscope surface files, not just solved molecule ones:

http://www.emdatabank.org/

Permalink Reply by Nik Willmore on April 20, 2016 at 9:05am

...also, PDB models often lack the full often radially symmetrical assembly, only giving one unit, and I don't know how to recreate the full protein machine like the PDB page often indeed shows fully assembled.

Permalink Reply by Nik Willmore on April 20, 2016 at 10:48am

Today's highlight was a heat shock protein cluster, for instance, but loading it into iMolview only gives one unit:

https://twitter.com/PDBeurope/status/722671886333841409

Permalink Reply by Nik Willmore on April 29, 2016 at 7:11pm

Ryan, your download link is failing for both your plug-ins:

"Error: INSERT INTO users (first, last, email, field, comment, date, timestamp) VALUES ('Nik', 'Willmore', 'nikwillmore@gmail.com', '', '','2016-04-29 20:39:48 Friday','1461976788' )"

Permalink Reply by Ryan Hoover on May 1, 2016 at 5:36pm

Thanks for letting me know, Nick. It is fixed now.

Permalink Reply by Nik Willmore on May 1, 2016 at 9:52pm

New problem: the Protein tab is missing that I see here in your screenshot, but the rest is intact.

http://www.ryanhoover.org/images/Alba_Demo_GFP_DNA_TxTl_ProteinQuer...

Tried with both latest Rhino/Grasshopper and Rhino 6 WIP. No files were blocked in Windows. Using 64 bit Windows 7. Tried placing folder in User Objects as well as individual folder contents. There are 43 files, which is indeed 4 files short of how many components you show.