Tag: ned seeman

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NanoEngineer-1 Version 1.1.1 – Still A Go-To In Ubuntu 24.04

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

With great thanks to Bryan Bishop for keeping his github account alive, a very old version of NE1 sitting on a fresh install of Ubuntu 24.04.

Sixteen years (!) since its release, it's still something I return to regularly because it does a very specific set of operations very well (I'd say that even if I didn't help with the development). Having made the leap on one of my machines to get used to anything new in 24.04 ("Noble Numbat." And re-testing all my other usual apt-gets to see what else I'm using from a decade ago that still has a chance of loading), trying NanoEngineer-1 (NE1) was on my short list of "if this doesn't work, I ain't upgrading" apps.

Bryan Bishop's github repo for Version 1.1.1 is alive (some highlights from the old gallery included) and the program is still kicking with this new install. I note that googling "NanoEngineer-1" now takes you to his page first above others, which is great.

This post is just an FYI – NE1 still runs like a charm. From his download link and how-to, it's a simple few steps.

My only installs on 24.04 include:

sudo apt-get install mesa-utils libx11-dev

And I'm not entirely sure about needing the libx11-dev. The snippet below taken from the github readme will have you running:

# download the ready-made chroot archive (600 MB)
wget http://diyhpl.us/~bryan/irc/nanoengineer/nanoengineer-chroot.tar.gz

# extract the chroot
tar -zxvf nanoengineer-chroot.tar.gz

# mount these things if you want the GUI to work
for i in etc/resolv.conf tmp proc dev; do sudo mount --bind /$i nanoengineer-chroot/$i; done

# allow connections from other uids over the local X11 socket
xhost +local:

# jump in
sudo chroot nanoengineer-chroot/

# now run nanoengineer
su nanoengineeruser -c "python ~/code/nanoengineer/cad/src/main.py"

And with that, NE1. No effort to optimize, I've not tried loading a REALLY BIG mmp file to see what might crash, but I'm happy to have at least three or four more years of access to my old mmp ("molecular machine part") files before, at worst, jumping to VirtualBox.

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Structural DNA Nanotechnology Graphic Featured In TASCHEN's "Science Illustration"

From the "keep it in the gallery because it might come in handy someday" department:

I'm very pleased to make mention of ye olde Nanorex's "Structural DNA Nanotechnology" poster now appearing in another venue that isn't this site or my office wall. The graphic is featured on pages 414-415 of the new TASCHEN book "Science Illustration. A History of Visual Knowledge from the 15th Century to Today," complete with the entirely reasonable name-drops of Richard Feynman (who I've published with before) and K. Eric Drexler (who I've also published with before).

As an aside, my appreciation of TASCHEN books began with my buying a copy of Andreas Cellarius: Harmonia Macrocosmica (which is priced a lot higher now than it was then) at the Los Angeles Griffith Observatory gift shop back in 2007 – an equally weighty tome that I still dragged around the place for an hour or more just to make sure that last copy was mine. I've seen smaller coffee tables in my day than either of these books (making the use of coasters all the more important should you choose to purchase either).

The author Anna Escardó is happy, my old boss Mark is happy, I'm happy, and now you, too, can stare at the image in a wonderful new book and lament Ned Seeman never having been flown out to Stockholm in acknowledgement of laying the foundation for an entire interdisciplinary branch of science.

"If you don't like it, buy a copy for someone you don't like." – Dafnis Prieto