Request for Atom Renaming Feature Before PDB Export in Avogadro

General Discussion Suggestions
1

In Avogadro, it would be very helpful to have a feature that allows users to rename atoms after building the structure and before exporting it to a PDB file. This functionality would improve clarity and make it easier to identify and understand specific atoms during subsequent simulations or analyses.

Thanks and regards
Sachin Kumar Varshney

2

Rather than post-export rename, which seems like it’d be confusing (would be hard to know which atom is which), perhaps any custom atom labels that have been added could be used for the PDB?

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3

That seems like a good idea. I think the question with using the custom atom labels that way is how to label the resulting HETATM or ATOM records (i.e., likely HETATM).

@varshney - can you give me an example of what you’d want to see in the PDB export?

4

Also, would this be better suited for PDBQT format support instead of PDB?