Hello Maher, this means your PDB file contains a molecule that cannot be matched against known molecules in Phenix dictionary. Can you please send me PDB file and I will be able to tell more. Pavel On 12/3/14 10:55 AM, maher alayyoubi wrote:

Hi Everyone,

I am having a problem of phenix.refine not accepting a pdb file that I just finished editing in coot. It is a protein RNA compplex where the protein part was built in buccaneer and the RNA strand built in nautilus. I assembled the final model by text editing the pdb file and adding the RNA part.

Whenever I feed this pdb file into phenix, it comes back with two errors: " number of atoms with unknown unbonded energy type symbols:6" . "The coot command could not be located"

Does anyone know how to fix this problem?

I tried converting the file into mmcif and feeding it to phenix but the same error comes back again.

Thank you very much,

Maher