Dear Coot Developers,
I found a bug in Coot 1.2 where atoms added via Modelling → Add An Atom are
written to mmCIF with an empty label_atom_id, which phenix.refine rejects
("unknown nonbonded energy type symbols").
Steps to reproduce:
Open 2fna.cif
Delete one Mg²⁺
Modelling → Add An Atom → Ca, click in the map
Save coordinates as .cif
Run phenix.refine on the file
Observed CIF line:
HETATM 6175 CA . . --- . 1 -32767 . . 21.014 52.249001 86.676003 1 30
? ? ? ? ? ? 1 CA C CA 1
label_atom_id is . and the atom is rejected.
Expected: label_atom_id populated with the atom name, e.g.:
HETATM 6175 CA CA . --- . 1 -32767 . . 21.014 52.249001 86.676003 1 30
? ? ? ? ? ? 1 CA C CA 1
Saving as PDB works fine; manually editing the CIF to fill label_atom_id also
makes phenix.refine happy.
Please let me know if you need any additional information to reproduce this, or
if you would like to discuss further.
Thank you in advance for looking into this.
Best regards,
Michal Gucwa
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