iiinova — where your digital self keeps evolving

Geoff Hutchison @geoffhutchison.net · 11/09/2026

On the walk to my office today, #Pittsburgh Soldiers and Sailors Memorial has a tribute with 7,087 dog tags representing the service members lost in the "War on Terror" after September 11, 2001.

Photo of Soldiers and Sailor's Memorial Hall in Pittsburgh's Oakland neighborhood, in the middle of Pitt's campus. Hanging across the walkway are 7,087 dog tags representing the lives lost since September 11, 2001 in the conflicts in the War on Terror

060

Geoff Hutchison @geoffhutchison.net · 29/08/2026

Ratings of Avogadro v2 improve the more people use it - probably because the final 2.0 release was *better* than earlier betas. If you've had problems, try a continuous nightly build: avogadro.cc/install

A table indicating ratings of Avogadro v2 - regular users, a few times, maybe once or twice. For "regular" users n = 32 responses, speed is 4.0 out of 5, Ease of Use is 3.85 out of 5, and Stability is 3.81 out of 5. For "a few times" users n = 10, speed is 4.0 out of 5, ease of use is 3.4 out of 5, and stability is 3.5 out of 5.

100

Geoff Hutchison @geoffhutchison.net · 20/05/2026

Had a great time at last night's @brucespringsteen.net packed concert in #Pittsburgh - including Ghost of Tom Joad and others with @tommorelloofficial.bsky.social Heard a lot of local cheers for Youngstown Came home feeling better than I have in weeks - "Hope and Dreams"

Janky, blurry concert snapshot from PPG Arena in Pittsburgh of Bruce Springsteen "Land of Hopes and Dreams" concert on May 19th

0111

Geoff Hutchison @geoffhutchison.net · 03/04/2026

Thanks! That was interesting. Once I got it in, the rendering wasn't breaking a sweat even with real-time shadows. OTOH, it attempted to guess bond orders which would have been pretty slow, so I hacked the code to turn that off. (I'll add support for assemblies too.)

Avogadro2 rendering of PDB entry 9MBO reconstructed assembly

230

Geoff Hutchison @geoffhutchison.net · 26/02/2026

I share the sad news that Prof. David H. Waldeck passed away after a battle with cancer. Dave was an extraordinarily creative scientist, a devoted educator, and to all of us a friend, mentor, and leader. He will be deeply missed #chemsky #chemchat

Photograph of David Waldeck - in the background is the University of Pittsburgh's Cathedral of Learning

7236

Geoff Hutchison @geoffhutchison.net · 19/02/2026

I decided to see what Claude Code code do on this. - It pulls RSS feeds (& import OPML) - It claims to rank my thumbs up - It keeps my "I want to read this" instead of 100 open tabs I don't know how well it actually ranks, but 🤷‍♂️ If it seems useful, let me know... github.com/ghutchis/rss...

Screenshot of vibe-coded "RSS Ranking" tool Dispatch indicating a set of unread journal articles, "Bookmarked" articles including [ASAP] General-Purpose Models for the Chemical Sciences: LLMs and Beyond

020

Geoff Hutchison @geoffhutchison.net · 30/01/2026

Literally anyone can now load up a #compchem calculation, cube, etc. and display results either as conventional isosurfaces, wireframes, or volumes.

Caffeine molecule rendered as an electron density volume, showing red "clouds" for electrons

1111

Geoff Hutchison @geoffhutchison.net · 30/01/2026

Obviously a lot is going on (gestures widely) Amid chaos, I cope by doing *something* -- anything. Lately, it's been coding for @avogadro.cc because it feels like some small change I can do myself For *years* I've wanted to show electron density volumes .. little clouds ☁️☁️ #compchem

Rendering of highest occupied molecular orbital (HOMO) of a conjugated molecule showing conventional orbital isosurfaces in red and blue bubbles.

Rendering of highest occupied molecular orbital (HOMO) of a conjugated molecule showing volumetric electron density in shades of red and blue clouds

55812

Geoff Hutchison @geoffhutchison.net · 06/10/2025

Tested out some water clusters during lunch. - MMFF94 has point charges and hydrogen bonds - UFF does not (so water molecules push apart) At some point I'll add some simple dynamics… #compchem #compchemsky

3152

Geoff Hutchison @geoffhutchison.net · 13/05/2025

Yeah, I need to do a "open URL to get the oAuth token" piece first. That's a useful example for a range of services. And yes, the idea would be to allow users to call directly from the GUI (e.g., get back Chemeleon unit cells)

Screenshot of Avogadro app showing a Coordinate Editor window on the left with three atoms and Cartesian coordinates, as well as a unit cell of MgB2 to the right

020

Geoff Hutchison @geoffhutchison.net · 07/03/2025

Hey #Pittsburgh - come join everyone here in Schenley Plaza to #StandUpForScience

05710

Geoff Hutchison @geoffhutchison.net · 07/02/2025

Hey #Pittsburgh folks - consider seeing __Trouble in Mind__ at the Pittsburgh Public Theater - now until Feb. 23rd. We went last night -- happened to also be #DivineNine night! Fantastic production. ppt.org/production/9...

Stage of Pittsburgh Public Theater's production of Trouble in Mind by Alice Childress, with a final quote by the playwright "I continue to create because writing is a labor of love and also an act of defiance, a way to light a candle in a gale of wind."

010

Geoff Hutchison @geoffhutchison.net · 10/01/2025

I was laughing and my grad students suggested asking ChatGPT for a premise.

In the opulent glow of Santa Barbara’s gilded age, Ethyl and Methyl Dubbs, the radiant daughters of industrial titan Carbon P. Dubbs, find themselves the catalysts of a social reaction at the height of the season’s grand soirees. Amid the glittering chandeliers and alchemical whispers of the elite, Ethyl, a spirited debutante with a penchant for experimentation, finds her heart combusting for a dashing engineer whose wit is as sharp as his slide rule. Meanwhile, Methyl, the quieter but no less volatile sister, forms an unexpected bond with a poet whose words spark her imagination like a volatile compound. As rival suitors and family obligations threaten to destabilize their bonds, the Dubbs sisters must decide whether love is the true element they seek—or if their futures are destined to evaporate under the pressure of society’s expectations. In a tale where passion combusts, hearts react, and love bonds endure, the Dubbs sisters discover that chemistry is far more than science—it’s destiny.

100

Geoff Hutchison @geoffhutchison.net · 09/01/2025

That's what's great about the @avogadro.cc plugin - it will install xtb / crest for users if it's not installed. In a few weeks, I'll have code for submitting batches of molecules / conformers for ORCA, Gaussian, etc. or running them at once (e.g., GPU) via AIMNET from @olexandr.bsky.social

Screenshot of Avogadro2 showing Extensions menu and xtb plugin submenu with commands for optimize, conformers, energy, frequencies, molecular dynamics, orbitals, help, etc.

3144

Geoff Hutchison @geoffhutchison.net · 12/12/2024

After the recent ground-breaking AI-generated textbook, I wanted to try making #chemsky cover art too 🤔 Enjoy (lol) Cover art for a college textbook entitled "Physical Chemistry: Quantum Mechanics and Thermodynamics" featuring images of molecules, the Schrödinger equation, free energy and entropy

AI generated image - "Cover art for a college textbook entitled "Physical Chemistry: Quantum Mechanics and Thermodynamics" featuring images of molecules, the Schrodinger equation, free energy and entropy"

370

Geoff Hutchison @geoffhutchison.net · 19/11/2024

Why has no one posted the Rocinante from The Expanse?

The Rocinante starship from The Expanse series of books and show

010

Geoff Hutchison @geoffhutchison.net · 17/11/2024

Not sure these quick photos (phone wires and all) do justice to today's sunset here in #Pittsburgh It was a nice end to an afternoon run though. 😉

Sunset view in Pittsburgh on November 17, 2024 with beautiful orange, red, pink colors reflecting off a few clouds and some blue sky

050

Geoff Hutchison @geoffhutchison.net · 16/11/2024

I know it's not the point, but that image looks like it has 2 bonds to a hydrogen...

Ball and stick molecular rendering of LSD molecule

110

Geoff Hutchison @geoffhutchison.net · 15/11/2024

Welcome to all the newcomers to #ChemSky 🧪 I don't post much, but you'll get a dose of #compchem and materials discovery, a bit of #machinelearning (with skepticism) and some sprinkling of #Pittsburgh (including @pitt.bsky.social and @pittchem.bsky.social) Enjoy some recent @avogadro.cc renders

Image of an endofullerene - a translucent sodium atom encased in a C60 buckminsterfullerene molecule, rendered by Avogadro

Image of a zirconium metal complex with a translucent green sphere representing the Zr metal ion interacting, labeled by Zr characters, bonded to two cyclopentadienyl rings, a methyl group and a hydrogen

1814

Geoff Hutchison @geoffhutchison.net · 05/12/2023

Thrilled to post the latest work by Omri Abarbanel - a *major* step forward for micro-pKa prediction models: QupKake has prediction errors ~0.5-0.7 by combining ML and QM 🧪 #compchem Omri beat commercial teams .. hire him 😉 We'll be sharing the model and all raw data soon. doi.org/10.26434/che...

Bar chart showing the performance of QupKake model against multiple previous works on two data sets, showing RMSE of 0.54-0.79 pKa units

1100

Geoff Hutchison @geoffhutchison.net · 27/11/2023

As someone who went to grad school as an inorganic chemist, it gives me some pleasure to finally have a free tool to click-click-click assemble iron bipyridine complexes or Ziegler-Natta catalyst models in @avogadro.cc in about the same time it takes to build an organic compound. #chemsky 🧪

Image of trisbipyridine iron(II) complex

Image of zirconium Ziegler-Natta catalyst with Zr atom bonded to two eta5-cyclopentadyenyl ligands, an eta-2 ethylene ligand, and a methyl group

061

Geoff Hutchison @geoffhutchison.net · 17/11/2023

Yes, although I think their table of "paper sources" illustrates that clearly. They have 3m articles from PubMed Central and 2m articles from arXiv. A lot of the rest is mostly abstracts. So the open question is "if LLM can read more papers does it stop hallucinating?"

Table of "paper sources" for Galactica large language model (LLM) e.g. https://arxiv.org/abs/2211.09085

220

Geoff Hutchison @geoffhutchison.net · 17/11/2023

Hi #chemsky - I could use some help I added a tool in @avogadro.cc to build metal complexes, including preview images of the ligands. The auto-generated ligand images for multidentate ligands look horrible. Anyone have ChemDraw of cyclam & triphos? discuss.avogadro.cc/t/help-neede...

101

Geoff Hutchison @geoffhutchison.net · 28/10/2023

Lots of changes, including: - Real time shading and ambient occlusion - New tool for inorganic complexes and "add a phenyl here" - Support for 3Dconnexion "space mouse" - Integrated support for Orca output - New forcefield framework

Molecule showing close-contact and real-time-shading in Avogadro

Gold nanoparticle showing real-time shading

Molecule graphic showing hydrogen bonding between DNA base pairs

130

Geoff Hutchison @geoffhutchison.net · 27/10/2023

Okay, I admit. I'm now taking "molecular modeling" very literally. Really happy with the new multi-color 3D printer I got for the lab. Looking forward to using physical models the next time I teach symmetry.

2151