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 Ryan Hoover on May 2, 2016 at 4:18pm

Hi Nick,

Thanks for catching these errors. The protein tools and one other simply dd not make it into the build somehow. This has been fixed and you can download the full package now.

Thanks for pointing out the issue with gHowl too. I had forgotten that I was using the gHowl XML parser in the PDB Query tool. I decided to simplify that for the user and wrote my own version. It is more specific to the RCSB query reply, which may make it a little more robust. The nice thing about these changes is that I was able to get it the full query cycle to run about 20x faster. While I was in there working on the protein tools, I made a few other upgrades. The PDB Open tool will now take a PDB ID as an input and and download it from RCSB. The Protein Ribbon visualizer now allows you to move and orient the protein. There were a few other tweaks that would only make sense to point out if you had already been working with these tools.

I appreciate your feedback thus far. I look forward to hearing more once you have the full package.

Cheers,

Permalink Reply by Nik Willmore on May 2, 2016 at 9:28pm

Impressed to learn ribbons are not just contained in the PDB file but require geometry testing of angles of the bond network.

I'm not getting great results yet though with either lysenin pore 5GAQ or the big ring 3J1W. Lysenin shows only one of the nine segments, oddly too since it seems to output more but on baking I don't see duplicates, maybe just a single duplicate ribbon collection. 3J1W gives a single unit too, but very oddly it is entirely flattened into the XZ plane.

These both take about 6 minutes to process, sorry, but symmetry does add up.

I've enclosed just my Python reader and the big ring, which proves the file itself contains all the units.

This is a different issue than my original lamentation that some PDB files lack the whole virus or whole cylindrical assembly, and I wondered how they 3D plotted the whole thing, where they got the symmetry information from.

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