Category: programs & os

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A NanoEngineer-1 Note (DNA Conversion Site, Recent Article, Related Links)

Above: A six-stranded triple-crossover (TX) DNA Junction. See Ned Seeman's ACS interview for more background.

Having just mentioned it in the context of making publication-quality pretty pictures, another brief note thanks to a citation request on the NanoEngineer Development/User Group (groups.google.com/group/nanoengineer-dev).

There's a website hosted at bionano.physics.illinois.edu for the conversion of NE-1 DNA mmp files to all-atom pdb ("Molecular Dynamics Simulation of Custom DNA Nanostructures Created by NanoEngineer-1") and NE-1's FNANO08 proceedings article ("NanoEngineer-1 – A CAD-based molecular modeling program for structural DNA nanotechnology") was included (with thanks to its use by German Barcenas) in the recent International Journal Of Molecular Sciences article "Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions."

The bionano site is a dramatic improvement from the NAMOT + sed'ing I worked up many years ago while getting something DNA-related stood up.

As a still-not-irregular user myself, I can appreciate the small hurdles needed to keep the program upright in modern OSs (or the need to just run VirtualBox and be done with it) – therefore noting both Bryan Bishop's dev page (worth the visit to github for the preserved gallery alone!) and Bruce Allen's Molecular Dynamics Studio effort and sourceforge-available download.

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Mac Mini + SSD = Happy. You Should Have Done This Years Ago.

It took me longer to reboot my well-out-of-Applecare 2014/2015 Mac Mini after a Monterey (OSX 12.1. Not even the upgrade to 12.2!) install than it did to:

  1. Say "f-it, this stinks."
  2. Pull a Crucial SSD drive from an unused Linux box
  3. Find my Mac-friendly tool set – it, like the alphabet, contains all the answers for the questions you might ask during this process. This Kobalt 20-Piece Kit does the trick (and more) if you can find it.
  4. Watch this video – https://www.youtube.com/watch?v=PDCt9M1KaIw
  5. Do the full upgrade with three brief pauses. I did not need the coat hanger trick. A few good pushes with the fingers on one hand was enough to dislodge the logic board.
  6. Cut, crimp, and run new cat6 from switch to entertainment center
  7. Run an Internet Recovery install (of Monterey)
  8. Set up two user accounts
  9. Transfer a full Photos library

As a parent with a toddler obsessed with trucks (20, to be exact), NASA and SpaceX launches, and (this month) Rush (The Professor!) concerts, the minutes saved on the reboots and youtube loading is worth its weight in gold-pressed latinum. The performance change is dramatic and the upgrade is completely worth your time.

Mark or Marc. I did not dig harder. Bless this man.