Above: Just needed an output from GaussSum for show-and-tell. This image from the article "Computational Study of Benzothiazole Derivatives for Conformational, Thermodynamic and Spectroscopic Features and Their Potential to Act as Antibacterials," available at https://www.mdpi.com/2073-4352/12/7/912.
Continuing on the Ubuntu 24.04(.1) migration theme and in the thick of needing a program to simply prepare partial Density-of-States (that link, but in this case for molecular systems) analyses, users might find themselves working through the python3, numpy, gnuplot, cclib, python3-tk installation process on the old GaussSumInstalling on Linux page without knowing that gausssum 3.0 has been available as a stand-alone apt-get for several recent Ubuntu versions.
apt-get GaussSum (3.0) after 502 MB of installs and one line change to preferencesbox.py
That, minus the amount of dependencies that get installed to make the program happen, is the good news.
First attempting to run gausssum from a terminal after this apt-get install produces the following:
user@machine:~$ gausssum
Traceback (most recent call last):
File "/usr/bin/gausssum", line 23, in <module>
import gausssum.gausssumgui
File "/usr/lib/python3/dist-packages/gausssum/gausssumgui.py", line 27, in <module>
from gausssum.preferencesbox import PreferencesPopupBox
File "/usr/lib/python3/dist-packages/gausssum/preferencesbox.py", line 21, in <module>
class PreferencesPopupBox(simpledialog.Dialog):
^^^^^^^^^^^^
NameError: name 'simpledialog' is not defined
Above: A six-stranded triple-crossover (TX) DNA Junction (again). See Ned Seeman'sACS 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.
And now for something completely different – composter tomatoes. This is year four of our producing far more tomatoes than we can possibly eat in a single season, leaving us to frantically scramble to find freezer space (we're not at the canning stage yet) while enjoying the fruits (no pun intended) of our limited labor. I've seen someinformation online about the ability to grow tomatoes directly in a compost pile, but I've never seen anyone report "you won't believe how many tomatoes we get doing this" anywhere, so thought I'd give it a shot.
For specifics, we're in the Rochester, NY area, falling somewhere in the 6b to 7a Hardiness Zone according to the newly updated (well, 2023) USDA website. Gardening prep (seedlings, seeds, indoor starters) starts in late April and we picked our last round of tomatoes this year (2024) in mid-October. Everything's organic – the food scraps that go in are organic and we don't treat our garden with anything except due diligence in tracking pests and possible disease.
Equipment And Preparation
Our raised beds are all 4 ft by 8 ft because 8 ft boards were the longest thing I could fit into my Honda Element. The composter is a taller version of the same and all kitchen scraps, yard cuttings, and leaves (and nothing else) go into it from end-of-tomato season to beginning-of-tomato season, with a cheap broom handle used to make holes to provide air down into the center (not even turning the stuff around, just a full dump with the colder weather).
The composter before sifting8ft x 4ft x 2ft, eight or nine times into six raised beds
The season starts around mid-April, where stuff in the pile gets shifted around and filtered for the currently six raised beds. The surrounding air is ripe with the smell of old citrus. Yes, some say don't add orange peels and the like – I suspect our soil is basic or "other" enough that its inclusion has had no detrimental effect. The composter gets knocked down by about a foot after this sorting is done. All of the broken-down compost below is out to the raised beds, all of the not-as-broken-down stuff is shifted into the holes left over from the sifting.
Tomato plants in on 15 May 2024. Start the clock.
After the leveling's done, one thin layer of dirt goes on top. Two – tops – bags of organic garden soil to make a 1" layer, basically just covering the kitchen scraps not broken down (almost just to make ascetically pleasing). Depending on the other yard work, that extra dirt just comes from trenching before mulching around the house.
This sized bed is just right four tomato plants and four tomato trellises at the beginning, but becomes a jungle by two months in. It gets so bad (see below) that one wonders if it wasn't better to just go with three. We deal with the crowding and overgrowth by convincing ourselves that we're still getting plenty of tomatoes.
First Month And Reinforcement(s)
One month in and the four plants have rendered the composter almost unrecognizable. Ten more days and the plants are hanging off the side. The reinforcement process includes extra horizontal bars and posts to keep the plants from hanging more so over the edge. Reaching inside is also a chore that risks breaking new growth, so the makeshift scaffolding goes in to try to keep the leaves elevated for reaching underneath to grab whatever's ripe enough.
Pic taken on June 13thPic taken on June 23rd
We tried to be extra-organized in 2022, but gave up because it was too hard to get to tomatoes without taking fencing apart. At this point, just some boards and posts to keep it reasonable.
Nice and organized and inaccessible, July 3rd 2022What works, July 15th 2024
First Collection
At left, we collected our first six really good tomatoes on July 27th of this year. On August 3rd, the collection at right. The August 3rd harvest then occurs every three-to-five days until late September.
How it started, July 27thHow it went after for the next almost-three months, August 3rd
From (what appeared on the outside as; see below) four plants, with this setup, in this climate, with a daily or other-day soaking, we eventually produced two heaping container fulls each week. The green beans are even more productive, but they're also cheaper, so will save for a future lazy day update.
The Mrs getting lost, August 13thThe youngest getting into the act, August 23rd
Blanching On The Cheap
We're into early September and are in the very low hundreds of tomatoes, having eaten many, given many away, making prep sauce to avoid canned tomatoes, and at some point being so tired that we just throw them into the freezer. Frozen tomatoes are great for cooking when your eldest doesn't like the consistency of tomato skins – heating these up makes the skin almost fall off (reverse blanching). The freezer is full, the COVID freak-out basement freezer is full, crisps and cobblers are being made to make room for more tomatoes, and we're damn-near sick of eating them at this point.
Approaching a full basement freezer with a month to go, September 11th.
Closing Up Shop
October 8th marked the end of the tomato plants this year, with a couple very cold evenings putting the production to rest. On clean-out, I discovered that the south-most tomato plant hadn't actually taken – something got to it early enough in the June grow-out that it got covered, stalk-broken, and didn't end up producing anything – so our harvest this year was only from three tomato plants and one or two cherry tomato plants that ended up growing behind our back from whatever was near the top in the composter as of May 15th.
Clean-up on October 8th. Note the avocado plant (one of six) under the owl as it observed the wealth of broken stalks.
Closing Costs
Not why we do it, but a good reason to consider doing it – the garden is our family escape some days and its watering is about the only time I can listen to a full podcast during the summer. That said, the current price for organic single tomatoes is $2.20 at our local large grocer. We paid $3.99 for each tomato plant, $9 this year for a bag of organic potting soil to finish the covering, and some amount into the water bill. At the current market rate, we grew over $400 worth of tomatoes this year and have a long, long way to go before we finish this year's crop.
