# Avogadro2 on debian/ubuntu: spectral plot (jkqtplotter) examples? **URL:** \ **Category:** Development\ **Created:** [June 28, 2026, 4:27pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481 "2026-06-28T16:27:10Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![RizzerOnGitHub](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/rizzerongithub/32/895_2.png) [@RizzerOnGitHub](https://discuss.avogadro.cc/u/RizzerOnGitHub)\ **Post date:** [June 28, 2026, 4:27pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/1 "2026-06-28T16:27:10Z")
jkqtplotter is now available on debian, and that means avogadro 2.0.0 is becoming available (ubuntu will follow soon after). It would be nice to be able to test that jkqtplotter is doing its job properly. Are there any available sample input files for generating the spectral plots that jkqtplotter enables? ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [June 29, 2026, 7:02pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/2 "2026-06-29T19:02:09Z")
> [@RizzerOnGitHub](#): > > Are there any available sample input files for generating the spectral plots that jkqtplotter enables? The easiest are any vibrational calculations, but also TD-DFT or NMR calculations with ORCA, for example. If you need some specifics, I’ll find a few and upload here. ---
**Author:** ![RizzerOnGitHub](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/rizzerongithub/32/895_2.png) [@RizzerOnGitHub](https://discuss.avogadro.cc/u/RizzerOnGitHub)\ **Post date:** [June 29, 2026, 7:19pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/3 "2026-06-29T19:19:45Z")
Anything simple is fine, just to check that the visualisation is working fine (by “input file” I mean the data file that avogadro would read, not the input file for the quantum chemical calculation 🙂 ) ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [June 29, 2026, 7:40pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/4 "2026-06-29T19:40:53Z")
Here are a few examples, including Raman, IR, and NMR: [spectra.tar.gz](https://discuss.avogadro.cc/uploads/short-url/3FZHsirpivEib95g4l1a2AfhQUV.gz) (100.8 KB) ---
**Author:** ![RizzerOnGitHub](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/rizzerongithub/32/895_2.png) [@RizzerOnGitHub](https://discuss.avogadro.cc/u/RizzerOnGitHub)\ **Post date:** [June 29, 2026, 8:17pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/5 "2026-06-29T20:17:42Z")
Looks likes it’s in working order. ![image](https://discuss.avogadro.cc/uploads/default/original/2X/9/9f96f1b3a24df3837c68d5f0fb01022f6c3a97a1.png) This is with jkqtplotter 5.0.0~beta2+git20260626.e82cd41. I needed some extra patches to be able to build on i386. caffeine.g98 however doesn’t seem to be working: the molecule loads but the Analyze “Plot Spectra” item is greyed out, as is “Vibrational Modes”. Maybe it’s a g98 reading issue rather than a jkqtplotter issue. Avogadro gets obabel (3.1.1) to read it as g92 ```auto OBProcess::executeObabel: Running "obabel" "-ig92 /build/test/spectra/caffeine.g98 -ocml" ``` But camphor and the two formaldehyde examples are showing their plots via “Plot Spectra”. ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [June 29, 2026, 8:37pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/6 "2026-06-29T20:37:33Z")
> [@RizzerOnGitHub](#): > > Avogadro gets obabel (3.1.1) to read it as g92 Any chance of `openbabel` 3.2.0, which adds `cjson` support? Looks like it’s already in `experimental`. (Which reminds me, I have to release a 3.2.1 shortly.) ---
**Author:** ![RizzerOnGitHub](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/rizzerongithub/32/895_2.png) [@RizzerOnGitHub](https://discuss.avogadro.cc/u/RizzerOnGitHub)\ **Post date:** [June 29, 2026, 11:06pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/7 "2026-06-29T23:06:41Z")
You’re right, openbabel 3.2.0 reads it as g98, ```auto OBProcess::executeObabel: Running "obabel" "-ig98 /build/test/spectra/caffeine.g98 -ocml" ``` The Plot Spectra option still doesn’t show for caffeine.g98 though. ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [June 29, 2026, 11:28pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/8 "2026-06-29T23:28:14Z")
> [@RizzerOnGitHub](#): > > The Plot Spectra option still doesn’t show for caffeine.g98 though Yeah, it needs to detect that `cjson` is available as a format with `obabel` (e.g., `JSON` support is compiled in). AFAIK, `cml` doesn’t have any support for spectra. ---
**Author:** ![RizzerOnGitHub](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/rizzerongithub/32/895_2.png) [@RizzerOnGitHub](https://discuss.avogadro.cc/u/RizzerOnGitHub)\ **Post date:** [June 30, 2026, 1:01pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/9 "2026-06-30T13:01:30Z")
> [@ghutchis](#): > > Yeah, it needs to detect that `cjson` is available as a format with `obabel` That’s an avogadrolibs to-do list item, right? If I use obabel on the command line to convert the caffeine.98 to -ocjson manually, then avogadro can read the caffeine.cjson file and is able to plot the IR spectrum. ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [June 30, 2026, 7:37pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/10 "2026-06-30T19:37:10Z")
The `obabel` pacakged with Mac, Windows, and AppImage all use `cjson` and have for several releases. If you’re getting `cml` conversions, that means when launched, `avogadro` didn’t see `cjson` in the list of available formats. I don’t know which `obabel` it picked, but it will default to `cjson` if available. ---
**Author:** ![RizzerOnGitHub](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/rizzerongithub/32/895_2.png) [@RizzerOnGitHub](https://discuss.avogadro.cc/u/RizzerOnGitHub)\ **Post date:** [June 30, 2026, 8:12pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/11 "2026-06-30T20:12:52Z")
Something very weird going on then. Here’s an example of the rest of the console output when trying to open caffeine.g98 from the gui ```auto $ avogadro Avogadroapp version: 2.0.0 Avogadrolibs version: 2.0.0 Qt version: 6.10.2 qt.core.qobject.connect: QObject::connect(QObject, Unknown): invalid nullptr parameter SSL version: "OpenSSL 3.6.3 9 Jun 2026" Using locale: "en_AU" qt Translation successfully loaded. AvogadroApp Translation "en_AU" loaded "/usr/bin/../share/avogadro2/i18n/" Extension plugins dynamically found… 49 registering obmm plugins OBProcess::executeObabel: Running "obabel" "-L formats read" OBProcess::executeObabel: Running "obabel" "-L formats write" OBProcess::executeObabel: Running "obabel" "-L forcefields" OBProcess::executeObabel: Running "obabel" "-L charges" OBProcess::executeObabel: Running "obabel" "-V" "obabel" found: "obabel: Open Babel 3.2.0 -- Jun 28 2026 -- 13:25:33" Checking for packages in "/home/user/.local/share/OpenChemistry/Avogadro/plugins" Checking for packages in "/usr/share/gnome/OpenChemistry/Avogadro/plugins" PackageManager::scanDirectory: directory does not exist: "/usr/share/gnome/OpenChemistry/Avogadro/plugins" Checking for packages in "/usr/local/share/OpenChemistry/Avogadro/plugins" PackageManager::scanDirectory: directory does not exist: "/usr/local/share/OpenChemistry/Avogadro/plugins" Checking for packages in "/usr/share/OpenChemistry/Avogadro/plugins" PackageManager::scanDirectory: directory does not exist: "/usr/share/OpenChemistry/Avogadro/plugins" Checking for packages in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/plugins" PackageManager::scanDirectory: directory does not exist: "/var/lib/snapd/desktop/OpenChemistry/Avogadro/plugins" Load registered packages Open Babel formats ready: 144 Setting default format to cjson. update comparing "2.0.0" to "2.0.0" OBProcess::executeObabel: Running "obabel" "-ig98 /build/test/spectra/caffeine.g98 -ocml" ``` So it does find Open Babel 3.2.0, and does declare default format cjson. Nevertheless it’s still calling `-ocml` when reading the file. It’s actually even weirder than that. If I repeat the exercise multiple times, it shows multiple variants of the Gaussian input format. There seems to be some randomness which one gets selected. I see variously -ig98, -ig03, -igal, -ig16, all with -ocml each time. ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [June 30, 2026, 8:24pm UTC](https://discuss.avogadro.cc/t/avogadro2-on-debian-ubuntu-spectral-plot-jkqtplotter-examples/7481/12 "2026-06-30T20:24:26Z")
> [@RizzerOnGitHub](#): > > I see variously -ig98, -ig03, -igal, -ig16 That’s not a big problem - it’s all the same code to Open Babel. Not sure why it’s using `ocml` though. I’ll look into it when I have a chance.