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

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.

Update: 24 February 2025

Because its use has come up in some recent twitter/X discussions (1, 2), adding the compilation of the good olde NE1 simulator engine to the mix to make NE1 fully-operational (albeit it a bit slow).

For the record, this process was written up for myself and others by the great Matt Moses. The sim owes its origin (talking waaay back) to the also great J. Storrs Hall.

From a fresh command line (or not, I'm just going through the rigorous process), the following:

sudo mount -t proc none proc
sudo mount -o bind /tmp tmp
sudo chroot ~/nanoengineer-chroot
su nanoengineeruser
cd code/nanoengineer/sim/src
make clean
make
touch *.pyx
make clean
make pyx
cd ../../cad
mkdir bin
cp ../sim/src/sim.so ./bin
cd ~
python /home/nanoengineeruser/code/nanoengineer/cad/src/main.py

And you should be able to minimize, adjust, and do simulations. When set to ND1 and not GROMACS. And on a single core. I told you it was old.