Error while reading file. Error, no molecule node found

General Discussion
1

Hi all, I installed Avogadro2 on Ubuntu 20.04, after I have saved the molecules in .cml format and try to open them, Avogadro gives me the following error: "Error while reading file … cml:
Error, no molecule node found ". How can I solve?

2

Can you send me some of the files? If you try saving to a different format (e.g., CJSON) does it work?

It’s strange considering CML is supported with internal code…

3

Hi ghutchis, I built the methane molecule, saved in cml format, then I tried to open the file with Avogadro but the error you see in the attachment appears.

Schermata a 2021-01-24 06-58-27
Schermata a 2021-01-24 06-58-271078×725 71.4 KB

On drive you will find the molecule file.

https://drive.google.com/file/d/1Ga58MlOXdnKP3_4Adoj4tesS0czZYjiG/view?usp=sharing

Thanks!

1 Like
4

Aha, I see. This is a CJSON with a CML extension. As a workaround, rename the extension and you should be good.

I’ll add some better error-checking in the “save file” code - if someone changes the extension to change the format.

{
  "atoms": {
    "coords": {
      "3d": [
        -1.60320246219635,
        0.8593167066574097,
        -3.969669819525734e-07,
        -0.8032059863735607,
        0.6109441697588549,
…