Geoff Hutchison 🧪💻

@ghutchis
418 Followers
421 Following
202 Posts
Chemist, Scientist, Husband, Dad, Runner, Teacher. I develop @AvogadroChem + @OpenBabel_org to find new materials for energy applications @Pitt_Chemistry he/him. Posting more frequently @[email protected]
Researchhttps://hutchisonlab.org/
ORCIDhttps://orcid.org/0000-0002-1757-1980
Avogadrohttps://two.avogadro.cc/
OpenBabelhttps://openbabel.org/
Geoff Hutchison 🧪💻Feb 11, 2024
Avogadro ProjectFeb 11, 2024

We're back with a new release! 🎉 v1.99 is out now

Highlights include improved force field optimizations, faster surfaces & orbitals, vibration spectra plots, and new tool icons, plus dozens of bug fixes, features, and new script plugins

https://discuss.avogadro.cc/t/avogadro-1-99-release/5271

#Chemistry #OpenSource #OpenScience

Avogadro 1.99 Release

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and many feature enhancements. Thanks to many for suggestions, bug reports, and discussions. Draft documentation can be found at https://two.avogadro.cc You can download Linux, Windows, and Mac versions at: Release Avogadro 1.99.0 · OpenChemistry/avogadrolibs · GitHub If you have comments or suggestions, please join us at https://discuss.avogadro.cc and as always, help and contributions in many forms ar...

Avogadro Discussion
Geoff Hutchison 🧪💻Dec 5, 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.

https://doi.org/10.26434/chemrxiv-2023-gxplb

QupKake: Integrating Machine Learning and Quantum Chemistry for micro-pKa Predictions

Accurate prediction of micro-pKa values is crucial for understanding and modulating the acidity and basicity of organic molecules, with applications in drug discovery, materials science, and environmental chemistry. This work introduces QupKake, a novel workflow that combines graph neural network (GNN) models with semiempirical quantum mechanical (QM) features to achieve exceptional accu- racy and generalization in micro-pKa prediction. QupKake outperforms state-of-the-art models on a variety of benchmark datasets, with root mean square errors (RMSEs) between 0.5-0.8 pKa units on five external test sets. Feature importance analysis reveals the crucial role of QM features in both the reaction site enumeration and micro-pKa prediction models. QupKake represents a significant advancement in micro-pKa prediction, offering a powerful tool for various applications in chemistry and beyond.

ChemRxiv
Geoff Hutchison 🧪💻Oct 26, 2023
Avogadro AnnouncementsOct 26, 2023
We are pleased to announce the latest release of Avogadro, including piles of bug fixes and many feature enhancements. This includes Patryk Skowroński from 3Dconnexion for contributing support for their devices. Thanks to many for suggestions, bug reports, and discussions. Draft developer documentation can be found at https://two.avogadro.cc You can download Linux, Windows, and Mac versions at: Discuss this on our forum.
Geoff Hutchison 🧪💻Oct 11, 2023
Avogadro General DiscussionOct 11, 2023
Can you help? While we have several almost-complete translations, we would love to see help with any of the following. Arabic (13%) Chinese (34%) Hindi (7%) Indonesian (42%) Italian (37%) Japanese (55%) Vietnamese (24%) It's easy - go to https://hosted.weblate.org/engage/avogadro/ and you can do a few translations at a time. Every bit helps a lot!

Discuss this on our forum.
Get involved in Avogadro!

Avogadro is being translated into 57 languages using Weblate. Join the translation or start translating your own project.

Hosted Weblate
Geoff Hutchison 🧪💻Oct 10, 2023
Show threadChemjobberOct 10, 2023
The 2024 Chemistry Faculty Jobs List (by Andrew Spaeth, me) has 365 tenure-track positions and 30 teaching positions: bit.ly/facultychemjobs2024 #facultychemjobs
Geoff Hutchison 🧪💻Sep 28, 2023
Avogadro General DiscussionSep 28, 2023
In Avogadro 1, we included some example files. For example, on Mac: Example Files: | | | |--- | ---| |1CRN.pdb | graphite.xyz| |2HHB.pdb.gz | morphine.cml| |benzene.fchk | nanotube.xyz| |c60.fchk | Pt <110>| | caffeine.g03| tpy-Ru.sdf| | | VitaminC.fchk| First off .. do you think it would be a good idea on Mac and Windows (and a download for Linux) to include some example molecules? If so, what are some examples to include? How many? 10? 20? 100?

Discuss this on our forum.
Including Example Files on Mac / Windows

In Avogadro 1, we included some example files. For example, on Mac: Example Files: 1CRN.pdb graphite.xyz 2HHB.pdb.gz morphine.cml benzene.fchk nanotube.xyz c60.fchk Pt <110> caffeine.g03 tpy-Ru.sdf VitaminC.fchk First off … do you think it would be a good idea on Mac and Windows (and a download for Linux) to include some example molecules? If so, what are some examples to include? How many? 10? 20? 100?

Avogadro Discussion
Geoff Hutchison 🧪💻Sep 27, 2023
Randahl FinkJul 4, 2023

I have often wondered why Putin's attack on #Ukraine angers me so deeply.

Walking on the beaches of Lillebælt, I realized it is because of this:

To this day, we Danes still see the concrete fortifications left by the Nazis on our shores, because 1 fascist leader got the insane idea, he had the right to topple our democracy.

He had no right. All he had was the delusion he was somehow supreme to everyone else.

We stopped the fascist in 1945.

We will stop the fascist now.

Geoff Hutchison 🧪💻Sep 18, 2023

We're hiring! Come join us in #Pittsburgh: two #facultychemjobs positions in #compchem and analytical chemistry, starting in Fall '24

#compchem: https://cfopitt.taleo.net/careersection/pitt_faculty_external/jobdetail.ftl?job=23007170&tz=GMT-04%3A00&tzname=America%2FNew_York

Analytical: https://cfopitt.taleo.net/careersection/pitt_faculty_external/jobdetail.ftl?job=23007176&tz=GMT-04%3A00&tzname=America%2FNew_York

Assistant Professor of Chemistry (Computational/Theoretical)

Click the link provided to see the complete job description.

Geoff Hutchison 🧪💻Sep 10, 2023
Avogadro DevelopmentSep 7, 2023
Right now, Avogadro 2 doesn't have a spectral dialog for vibrations, UV/Vis, NMR, etc. I'd like some feedback to rank / categorize which features are most important for development: For example... ## Most Important Apply shift (NMR) or scale (IR) Gaussian / Lorentzian broadening Export image Export data as CSV ## Nice to Have Import experimental data Label peaks Editing font size / bold / etc. Editing colors for background, axes, plots Other things for the wishlist?

Discuss this on our forum.
Feature Wishlist for a Spectra Dialog

Right now, Avogadro 2 doesn’t have a spectral dialog for vibrations, UV/Vis, NMR, etc. I’d like some feedback to rank / categorize which features are most important for development: For example… Most Important Apply shift (NMR) or scale (IR) Gaussian / Lorentzian broadening Export image Export data as CSV Nice to Have Import experimental data Label peaks Editing font size / bold / etc. Editing colors for background, axes, plots Other things for the wishlist?

Avogadro Discussion
Geoff Hutchison 🧪💻Aug 28, 2023
My thoughts are with the students, staff, and faculty at UNC Chapel Hill tonight. I know many at Caudill Labs. This has become a scene far too often at schools and universities in the US. #TooManyNames