I believe this to be a bug with Avogadro:
I cannot duplicate/copy-paste selected molecule.
Avogadro version: 1.100.0 / Qt:5.15.8
Operating system and version: macOS 15.6
Second molecule appear.
Nothing happens.
Draw a molecule → Select it with the ‘selection tool’ → Cmd+C → Cmd+V → No Effect.
Neither Cmd+D (duplication).
I don’t think this is a bug.
First off if you want to copy the whole thing, you don’t need to select anything. You only need to select if you want to copy some subset of the system.
The copy will have the same coordinates as the initial atoms. So you’ll have double the number of atoms and bonds, but you’ll want to move the new copy. (In v1.0, we gave a small random offset to make the copy visible but people didn’t like this.)
Once you’ve done the paste, either use the panel to move the new (selected atoms) to a specific position, or drag:
While having an offset for the new copy is useful for user discovery, it makes it much harder to create specific geometries (e.g., a dimer with X Å separation).
I am not able to copy. Either nothing happens or the error occurs:
Error reading clipboard data.
Detected format: Chemical JSON CJSON format is a lightweight intermediate format used to exchange information between Avogadro and other data parsing applications
Reader error: Error reading CJSON file.
Something is very wrong - CJSON is a native format. Can you upload an example file or a link to one?
Are you using 1.100 release or a nightly build?
An example file? There’s not a file. I just opened Avogadro, drew a molecule, and wanted to duplicate it. Avogadro 1.100.0 on MacOS Sequoia, as stated in the first message. There’s no written whether this is nightly build
If it just indicates 1.100.0, it’s not a nightly build. Here’s my current build - note that it indicates 1.100.0-125 (i.e., 125 commits past the 1.100 release) and a git hash g918b834. (The library version indicates 639 changes past the 1.100 release).
You can get a nightly build from Install — Avogadro 1.100.0 documentation
And you still receive that error about CJSON when copy / paste?
Can you save a file as CJSON?
