"Missing atom fragment" warning for atoms/fragments that are listed in the chemical component dictionary.

[dargen3]

Hello, I've encountered some strange behavior. When I tried to protonate a structure from the PDB database 3u5s. Hydride wrote out:

/home/dargen3/miniconda3/lib/python3.11/site-packages/hydride/fragments.py:212: UserWarning: Missing fragment for atom 'SE' at position 12 warnings.warn( /home/dargen3/miniconda3/lib/python3.11/site-packages/hydride/fragments.py:212: UserWarning: Missing fragment for atom 'SE' at position 136 warnings.warn( /home/dargen3/miniconda3/lib/python3.11/site-packages/hydride/fragments.py:212: UserWarning: Missing fragment for atom 'SE' at position 416 warnings.warn( /home/dargen3/miniconda3/lib/python3.11/site-packages/hydride/fragments.py:212: UserWarning: Missing fragment for atom 'SE' at position 528 warnings.warn( /home/dargen3/miniconda3/lib/python3.11/site-packages/hydride/fragments.py:212: UserWarning: Missing fragment for atom 'SE' at position 552 warnings.warn( /home/dargen3/miniconda3/lib/python3.11/site-packages/hydride/fragments.py:212: UserWarning: Missing fragment for atom 'SE' at position 771 warnings.warn( /home/dargen3/miniconda3/lib/python3.11/site-packages/hydride/fragments.py:212: UserWarning: Missing fragment for atom 'SE' at position 912 warnings.warn( /home/dargen3/miniconda3/lib/python3.11/site-packages/hydride/fragments.py:212: UserWarning: Missing fragment for atom 'SE' at position 1046 warnings.warn(

while residues with selenium atoms are present in the CCD dictionary and so their fragments should already be in the database. Is this the expected behavior, please?

[padix-key]

Hi, I am not able to reproduce these warnings. Can you post your code (or did you use the CLI?) and both, the Hydride and Biotite version you are using?

[dargen3]

Interesting. I couldn't reproduce it today either. Closing. If I come across the error again, I will reopen.