Bonding distances from PDB file changes


I have opened a PDB file in Avogadro in order to do QM calculations. However, when I open the file in Avogadro, certain bonding distances change compared to the input coordinates. It’s “only” about 0,05 Å, but it does make a difference in this case unfortunately. Why’s this, and can it be fixed?

Thank you in advance!

I don’t know of anything that would change interatomic distances at all.

Can you please give a bit more information?

  • Version of Avogadro
  • OS you’re using
  • Example file (e.g., through Google Drive, Dropbox, etc.)

Thank you so much for the input! I realized the issue was not with Avogadro now, which was right all along! The issue was with the other program I opened the PDB in… Sorry for posting before looking at that possibility thoroughly! Thanks again! And thanks for a great program! :slight_smile:

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