there are two issues I found using Avogadro1 and Avogadro2. Possibly related.
If I open a PDB file that was created with any kind of molecular software using A2, it opens just fine, but when I save it in A2, all the additional comments in the actual PDB gets lost (like TITLE, HEADER, REMARK …). I see that the version of PDB is different, but this tags are the same in latest and all previous versions.
In A1 I can open and edit and after saving these stay there like I expect they would!
I add these comments by hand.
If I try to reset the position of the molecule in A1 to 0.0.0 coordinates, I do get correctly positioned data in PDB file that works in A1, but when I open it again in A2 and save it, the coordinate system of the middle atom is not shown on 0.0.0 any more. Basically it opens differently then in A1.
Am I doing something wrong?
Thank you for your answers and great software.