Video Tutorials / Playlist

A recent post asked about older versions of Avogadro .. because there wasn’t a video playlist for Avogadro2.

I started putting together a list for the 2.0 release - which also serves somewhat for the revisions to the written website docs.

Thoughts? Missing topics? Things that are confusing?

(My intent is that I’ll finish up the AutoOpt tool so the toolbar / UI is more-or-less finished and then do a video a week or something.)

Intro & Building

  • Introduction & simple molecules
  • Import from PDB and name
  • SMILES and fragments
  • Inorganic and organometallic systems (with template tool)
  • Quick tips for building
  • Polymers and large structures
  • Peptides
  • DNA
  • Unit cells / materials

Optimizing

  • Basic Optimizing (including auto-optimize tool vs. optimize geometry, different methods)
  • Editing bond lengths, angles, etc.
  • Constraints
  • Conformers

Rendering

  • rendering options (including shadows, different styles, colors, etc.)
  • layers

Analysis

  • partial charges & dipole moment
  • orbitals
  • surfaces
  • vibrations
  • spectra (esp. vibrational, Raman, NMR, UV/Vis and CD)
  • symmetry

Crystals

  • Adding / editing unit cells
  • Importing crystals

Extensions

  • Input generators
  • Python & downoading / installing plugins

how to complement «Avogadro as shipped» by extensions/optional plugins which assist both working in Avogadro2, as well as with other programs (i.e. where Avogadro2 becomes a bridge to other projects).

An example could be the avogenerators to provide the necessary input files for a dedicated lab class with commercial programs (like Gaussian), or freely available (e.g., openMOPAC); or self-study (e.g., chemcompute.org). The survey equally should provide a brief (topical) note on each of the other extensions; more like an appetizer to use them (and attract potential contributors to existing/future extensions) than a detailed how-to the documentation of the web site can provide.

Given recent discussions about how to correctly set a suitable Python interpreter, deployment with pipx/conda, etc., a corresponding hint might be useful, too. Perhaps with an address pinned right below the video to link to the corresponding web site with additional documentation.

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I think we’ll have a reasonable solution for that soon. As I mentioned, pixi will now be bundled with the macOS and Windows packages, and at launch will ask about installing a default environment. As long as a user agrees and has an active network connection, it should work.

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Okay, I recorded a first video, including uploading the subtitles. It’s not yet publicly listed at YouTube - I’m curious to get feedback and suggestions.

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The content of the presentation was clear, the slides not too busy and well legible down to 360p resolution. The demo contains an attractive example Avoagdro2 both about the rendering style per sé, as well convincing about the management of large biomolecules. Because the installments address new users, I would like to recommend to lower the pace of the speech to about 0.85 of the current level.

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Good points. Particularly the speed of the voiceover - presumably some users who are not native English speakers will watch.

Maybe there’s an easy way to tweak the playback speed – syncing the recording was trickier than I expected.

For audio tracks I remember playitslowly, and later VLC player with a similar adjustment (coarse/fine) for audio/video (playback → speed) without too much affect on the pitch of a speech.

Hence I speculate this could be a task for ffmpeg – see for instance this example in their documentation – freely available, with the advantage (vs. clicks in a GUI) of a uniform deployment documented by the code applied. As long as there are enough data points per recorded time.

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Yes, it looks like I can probably do something like this:

ffmpeg -i input.mp4 -filter_complex "[0:v]setpts=1.18*PTS[v];[0:a]atempo=0.85[a]" -map "[v]" -map "[a]" output.mp4

I’ll experiment a bit.

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Youtube has the ability to adjust the playback speed built in so I wouldn’t stress about this, users can slow it down themselves if they like :slight_smile:

I’m not too worried about it. But I’m going to create separate channel for Avogadro videos, so I’ll see if the ffmpeg trick worked out okay. If not, I’ll post the original version and let people tweak the speed as they wish.

I liked the video. The only thing I wonder is if the layout will suit the future episodes. I like the logo, nice and consistent but it might a bit to big if you want to fit more data on a “slide“ later on.

Glad you appreciated it. Trying to get another one out soon.

I definitely thought about that. My conclusion was that if it keeps me from putting too much on a slide, that’s a good thing for the videos.

If anything I’d rather keep the fonts big and amount of text small, based on other YouTube like TED or Khan Academy.

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I should mention that there’s a new channel for these videos:

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