Improve way that users discover Avogadro?

I have noticed that when users come to the forum looking for support/troubleshooting, they are extremely frequently using Avogadro 1.2. I suspect this is because the existence of Avogadro 2, and where to download it from, is somewhat hidden to new users…

Googling “avogadro software” gives the website,, as the first result. I should think most people hear of avogadro by word of mouth, either on or offline, and thus surely google and then the official website must be the primary way people are introduced to avogadro. However, clicking the download button on the main avogadro website directs the user to sourceforge where an automatic download of Avo 1.2 begins. I think this may be why most new users end up using 1.2, and this surely hurts user retention as Avo2 is so much more stable and capable. Can I suggest that the download button instead links to GitHub, to the latest release page? Or alternatively, to, where the options are well laid out?

Equally, the second link on google is to the sourceforge page, not the GitHub page. Is there a way maybe to also deprecate the sourceforge repository in search engines in favour of the GitHub one?

The same applies to the “manual” link on the homepage. At the moment this links to the docs for Avo1.2, but this is of course now hopelessly out of date. I know the new docs are not yet comprehensive, but maybe it is worth redirecting the link to them already/in the near future?

Avo2 is still in beta, sure, but looking at the number of times you @ghutchis have to tell people to download a newer version, it is clearly currently too difficult for people to find. You must be tired of typing the same response to people every time! :smiling_face_with_tear: Thoughts?

We’re almost there… really, really close.

At the end of last summer, the survey suggested that a lot of people hadn’t tried Avo2 yet because it was missing feature X or Y or Z.

  • various bugs (mostly fixed)
  • molecular surfaces / electrostatic potentials (now in 1.97)
  • translation support (now in 1.97 … annoying :beetle: finally squashed)
  • hydrogen bond rendering (now in 1.97)
  • optimization / auto-optimization with frozen atoms and constraints (coming soon)
  • etc. (probably a few other things I’m forgetting right now)

And of course, updated documentation / website / tutorials.

I’ll be posting a thread on “simple things you can do to help” soon.

My semi-realistic goal is to get a 2.0 release by October. I’m pretty sure SourceForge will disappear over time, but we’ll also post releases there.

One thing that would really help is for someone to figure out a “one-click download”

Like if I go to Download — - it knows I’m using a Mac or Windows machine.

I want something like that using Python (Sphinx) or JavaScript…

Some users, like me, may know that Avo2 exist and still use Avo1.

Is there a particular reason? Missing feature? Bug?

A few. Keep in mind I’m a beginner in computational chemistry so I may not appreciate software being able to do some peculiar advanced stuff and my demands are quite low-level ones.

To be honest, I was slightly annoyed (to the extent that I didn’t want to open it anymore) when I first opened Avo2. The very first thought that came to my mind: where are all the features?

  1. No Auto Optimization Tool in header. I used Avo1 90% of the time to build a molecule prior to starting a QM job, so I mostly used the Optimizer. Yes, you can still do it with a shortcut or reach into Extensions → Open Babel (which is very unintuitive), but I liked having a separate small Window where I could always start/stop optimization, make sure I use the proper force field or change the algorithm. I can do that in Avo2 by going to Extensions, but in Avo1 it was done much better in terms of UI/UX. I do appreciate the increase in speed though.
  2. I still don’t understand the reason for having Layers (a window which takes 50% of the sidebar on Launch). Yes, I can build different molecules in different Layers, but then? Whenever I tried to open Input Generator on any multilayered file the program crashed.
  3. Display Types don’t have the wrenches, like they used to. At some point the additional “view configuration window” started to show up, but it only works half the time. And for things like VdW spheres I still don’t know how to change opacity.
  4. There were times when I could simply open an output file and see orbitals/vibrations pop up immediately. I still don’t know how to visualize MOs or vibrations in Avo2. To be fair, Avo1 also stopped doing that properly after one of the macos upgrades, but that was the reason I switched to another program and I was really hoping Avo2 would fix those issues.
  5. I don’t know how to do Constrained Optimization in Avo2 (or if it’s even possible).
  6. Conformer search in Avo1 was far from being exhaustive, but it was still useful. I don’t think it’s present in Avo2.
  7. Didn’t find AutoRotation in Avo2.

Whenever I say I don’t know I mean that I could figure it out in Avo1 fairly quickly (without reading docs), but could not in Avo2.

Interesting. I think you have a point as far as discoverability. I was going to ditch it in favor of a check / uncheck in the menu bar, but it’s worth doing both.

As I mentioned, the new optimization framework is coming. It will bring back constraints and auto-optimization, while enabling you to use other programs / ML potentials etc. for optimization too.

Interesting. Haven’t seen that one, but I’ll look into it.

Analysis => Create Surfaces… or Analysis => Vibrational Modes…

The “pop up docks” were useful, but have been further down the “finish 2.0” checklist.

Believe it or not, I hadn’t noticed there wasn’t a conformer search command in the Open Babel extension. (My group has a whole separate conformer infrastructure.)

Feedback is helpful - not least because I don’t know what I don’t know (e.g., particular features that are keeping people from switching). Which is the point for the forum and for Issues · OpenChemistry/avogadrolibs · GitHub

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Also, most people who used Avogadro for teaching actually liked seeing the animation of how molecule responds to the force field and gradually reaches the local-min geometry. But I do agree that speed is more important for people who use it for QM calcs.

Thank you. But let’s compare the UX:

Avo 1:

  1. I take orca5.0 output file .out
  2. Drag&drop into Avo1
  3. I have the MOs (although they’re all black since macOS Catalina, or smth like that)

Avo 2:

  1. Can’t handle orca out file. You do orca_2mkl fname -molden. Not an issue since I usually do this for JMol
  2. An extra step, however, is renaming fname.molden.input to fname.molden because Avo2 refuses to open the former.
  3. For some reason, 50% of the time the file opens without tick next to Ball-and-Stick so you see white screen and unless you know what to look for, you may just think it doesn’t handle molden files properly.
  4. Now, you go Analysis → Create Surfaces. You create MO. But again you see nothing, because …
  5. You have to go to display type and enable meshes.
  6. Even then the orbital looks not the way it should!



Jmol (in two steps: open .molden.input and write mo homo)


  1. Now the fun part, let’s try to visualize F 1s.
    Why do I have duplicate options?

Notice how it’s also locked at MO 6 even though I visualized MO 5, and also you can’t switch from MO 6 to MO 1 unless you pick a different Molecular Orbital option in the surfaces dropdown.

Oh, wait, copies again…


I do understand this is normal for new software to have bugs or things not working properly. I’m only showing why a user may decide to stick to Avo1 at the current state of Avo2.

Also, I really appreciate the use of Discourse for this.

I had an impression Avo2 was developed by a completely different team: I found the app on a different domain and the github repo belongs to a different organization. Which is why I didn’t even bother to try & raise issues, as I thought: “well, those people may have completely different needs or design views”.

Also, I may not be representative of the target audience, but I found these two pictorials:


to be much more intuitive than


I mean, in hindsight, I can understand how they were developed, but because I was a user of Windows XP/7, the first icons clicked with me without any info from “highlights” and I never mistook one for another.

Oh, definitely. It’s one reason we’re calling releases 1.97 and not 2.0 :wink:

BTW, the 1.97 bug with the half-orbitals was fixed:

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