Error saving PDB files with Avogadro2

there are two issues I found using Avogadro1 and Avogadro2. Possibly related.

  1. 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.

  2. 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.

Avogadro v2 does not have much support for PDB beyond ATOM, HETATM and CONECT records. (Adding support for residues, sequences, etc. is on the need-to-do-soon list.)

So it’s known that fields will be removed if you save a PDB file in Avogadro v2.

As to the coordinates… it sees like you’re saying there’s a coordinate shift when saving?

A, I see, ok.

As for the coordinates. I think no! I see coordinate shift, but when opening. I save view z=0, it opens as xyz something in different programs.

Thank you, for your answers.