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Error saving PDB files with Avogadro2


#1

Hello,
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.


#2

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?


#3

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.

Matej