Hi thank you for your reply, I'm not working with ligand, but a complexe. I do not have hydrogen in my model, so it seems I have a bigger problem. [image: image.png] I tried to use PDB_REDO, however i'm using mrc format for my ED map Le jeu. 30 janv. 2025 à 16:39, Georg Mlynek a écrit :

Hi Yann, can you post a screenshot of the error message? It should be stated there which are causing problems.

Very often the problems are hydrogens. So just delete those. One easy way is to do is to open in coot and when saving there is a tick box without hydrogens. There are also tools in phenix doing this.

Also you can submit the pdb to PDB_REDO to check if there are more sever problems. If PDB_REDO runs then there are no big errors. Then just use the output for phenix refine.

And as Xavier wrote ligands also can cause problems. But also there most times the hydrogens.

Br, Georg.

Am 2025-01-30 um 4:26 PM schrieb [email protected]:

...

Hello, I'm a newbie phenix user, and i was trying to refine a model.

and when i tried to refine it, I got an error message saying that some atoms had unknown nonbonded interaction.

However, there are no indication to which one are problematic, Any tips on how to find the problematic one and how to correct them ?

best wishes, Yann _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s